From chemistry-request@server.ccl.net Mon Apr 28 16:04:20 2003 Received: from web15208.mail.bjs.yahoo.com ([202.3.77.138]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3SK4Fo31923 for ; Mon, 28 Apr 2003 16:04:16 -0400 Message-ID: <20030428200406.17495.qmail@web15208.mail.bjs.yahoo.com> Received: from [218.30.18.116] by web15208.mail.bjs.yahoo.com via HTTP; Tue, 29 Apr 2003 04:04:06 CST Date: Tue, 29 Apr 2003 04:04:06 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: problem with GAMESS on FreeBSD To: CCL , Gamess MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I have a preblem with GAMESS on pc running FreeBSD. I have compiled the GAMESS with f2c/gcc and g77/gcc, respectively. When I submit a job to GAMESS, it will give me the correct results. However, it will not terminate after it printed the message: EXECUTION OF GAMESS TERMINATED NORMALLY. When I kill the process it will add two lines to the output file (*.log): child process 0: interrupted by parent ddikick: trapped error SIGINT. Does here any one have compiled successfully the GAMESS on a FreeBSD platform, or have encontered such problems? Any suggestions will be very appreciated. Thanks a lot in advance. Regards, Jinsong P.S.: the gcc and g77 version is 3.2.1, f2c is 3.0, and the FreeBSD is 5.0 Release. _________________________________________________________ Do You Yahoo!? ÏÂÔØÃâ·Ñ¼´Ê±ÁÄÌìÈí¼þ¡°ÑÅ»¢Í¨¡±¸ÐÊܶ¯¸ÐÁÄÌì÷ÈÁ¦£¬¸Ï¿ìÓÃÄãµÄÑÅ»¢µçÓÊÕʺŵǽ°É~ http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.messenger.yahoo.com/ From chemistry-request@server.ccl.net Mon Apr 28 09:39:15 2003 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3SDdEo18169 for ; Mon, 28 Apr 2003 09:39:14 -0400 Received: by mailbox.engr.sc.edu with Internet Mail Service (5.5.2656.59) id ; Mon, 28 Apr 2003 09:38:45 -0400 Message-ID: From: "WANG, YIXUAN " To: "'zjwu'" Cc: "'chemistry@ccl.net'" Subject: RE: Re: CPCM TS location Date: Mon, 28 Apr 2003 09:38:44 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C30D8B.7CFE4640" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C30D8B.7CFE4640 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Please take a look at Wang, Nakamura, Balbuena, JACS, 2002, Vol. 124, = 4408. We had used PCM-B3PW91 in the paper as well as CPCM (to be published) = to optimize reductive decomposition TS (page 4410, structure 7) of = vinylene carbonate. =20 Yixuan Wang =20 Department of Chem. Engineering Univ. South Carolina=20 =20 -----Original Message----- From: zjwu [mailto:zjwu@ns.ciac.jl.cn] Sent: Thursday, May 01, 2003 8:27 PM To: help@gaussian.com Cc: chemistry@ccl.net Subject: CCL:Re: CPCM TS location Dear Dr. Hess, =20 Do you know any publications containing cpcm ts structure calculations? = I do find some papers on local minima optimizations using cpcm, but did not = see any paper on transition state calculation using cpcm model? =20 Any papers on this aspect are appreaciated. =20 Best wishes, =20 Zhijian Wu _____ =20 Dear Dr. Zhijian Wu, You have performed the steps I'd recommend, i.e. using the = gas-phase =20 Hessian or the Hessian from an Onsager calculation. Since these options = =20 did not work, it might be necessary to calculate the CPCM Hessian. You = cannot do this with "opt=3D(ts,calcfc)" in G98, but you can perform a =20 two-step job in which the first step uses "freq" and the second job =20 step uses "opt=3D(ts,rcfc)". You might also consider performing an =20 "opt=3Dqst3" calculation in which you use your Onsager model optimized = TS =20 as the initial guess structure for the CPCM transition state. =20 Regards, Jim Hess =20 On Thursday, April 24, 2003, at 01:13 AM, zjwu wrote: =20 >> Dear Dr. Hess, >>=20 >> ?/DIV>=20 >>=20 >> I mean the job failing because the structure is not the TS = structure =20 >> anymore. The calculation may converge but goes to different = geometry =20 >> which I did not want. I have tried to read force constants at cpcm = >> calculation from either gas phase frequency calculation or Onsager = >> frequency calculation (these frequencies are obtained based on the = >> optimized geometry) (calculation using Onsager model works well for = =20 >> the TS calculation).=A0In addition, I also tried opt=3D(ts,calcfc), = but as =20 >> you know,=A0calcfc does not exist for=A0cpcm.=A0It seems g03 is = possible to =20 >> calculate fc at cpcm level. >>=20 >> ?/DIV>=20 >>=20 >> Hope I have made myself clear. >>=20 >> ?/DIV>=20 >>=20 >> Thank you very much for your answer. >>=20 >> ?/DIV>=20 >>=20 >> Best regards, >>=20 >> ?/DIV>=20 >>=20 >> Zhijian Wu >>=20 >> ?/DIV>=20 >>=20 >>=20 >>=20 << image.tiff>=20 >>=20 >> Dear=A0Dr.=A0Zhijian=A0Wu, >> = =A0=A0=A0=A0Is=A0this=A0job=A0failing=A0because=A0it=A0runs=A0out=A0of=A0= optimization=A0cycles?=A0I'd=20 >> ?/DIV>=20 >> = need=A0to=A0know=A0more=A0details=A0about=A0what=A0is=A0going=A0wrong=A0= before=A0I=A0make?/DIV>=20 >> = detailed=A0suggestions,=A0but=A0one=A0possible=A0way=A0to=A0improve=A0th= is=A0c alculation?/DIV>=20 >> = is=A0to=A0calculate=A0the=A0force=A0constants=A0in=A0the=A0solution=A0ph= ase,=A0then=A0u se?/DIV>=20 >> = these=A0force=A0constants=A0to=A0start=A0the=A0transition=A0state=A0sear= ch.>.=A0Usually=A0t he=20 >> ?/DIV>=20 >> = gas-phase=A0Hessian=A0is=A0a=A0good=A0enough=A0approximation,=A0but=A0in= =A0some=A0c ases?/DIV>=20 >> = where=A0the=A0gas-phase=A0and=A0solution-phase=A0potential=A0energy=A0su= rfaces=A0a re?/DIV>=20 >> = different=A0enough,=A0explicitly=A0calculating=A0the=A0second=A0derivati= ves=A0in=A0t he?/DIV>=20 >> = solution=A0phase=A0can=A0be=A0helpful.=A0Incidentally,=A0if=A0you=A0are=A0= using=A0G98,=A0t he?/DIV>=20 >> = CPCM=A0second=A0derivatives=A0will=A0be=A0performed=A0by=A0numerical=A0d= ifferentiation?/DIV>=20 >> = of=A0the=A0analytic=A0gradients=A0and=A0if=A0you=A0are=A0using=A0G03,=A0= the=A0second?/DIV>=20 >> derivatives=A0will=A0be=A0calculated=A0analytically. >> ?/DIV>=20 >> Regards, >> Jim=A0Hess >> ?/DIV>=20 >> ++++++++++++++++++++++++++ >> James=A0Hess,=A0Ph.D. >> Customer=A0Support=A0Scientist >> Gaussian,=A0Inc. >> e-mail:=A0help@gaussian.com >> ++++++++++++++++++++++++++ >> ?/DIV>=20 >> ?/DIV>=20 >> On=A0Tuesday,=A0April?2,?003,=A0at?8:29=A0PM,=A0zjwu=A0wrote: >> ?/DIV>=20 >> > > =A0Dear=A0members, >> > >=20 >> > > ?/DIV>=20 >> > >=20 >> > > = =A0I=A0am=A0trying=A0to=A0locate=A0the=A0transition=A0state=A0using=A0cp= cm=A0model.=A0T he?/DIV>=20 >> > > = =A0initial=A0structure=A0is=A0from=A0gas=A0phase=A0optimized=A0transitio= n=A0s tructure?/DIV>=20 >> > > =20 >> = ?with=A0correct=A0vibrational=A0mode).=A0The=A0optimization=A0at=A0cpcm=A0= level=A0f ails?/DIV>=20 >> > > =A0by=A0the=A0following=A0keywords >> > >=20 >> > > ?/DIV>=20 >> > >=20 >> > > =20 >> = ?b3lyp/6-31g(d,p)=A0opt=3D(ts,=A0readfc,=A0noeigen)=A0scrf=3D(cpcm,solve= nt=3Dwater) >> > >=20 >> > > ?/DIV>=20 >> > >=20 >> > > = =A0Do=A0anybody=A0has=A0experience=A0in=A0cpcm=A0transition=A0structure=A0= c alculation? >> > >=20 >> > > ?/DIV>=20 >> > >=20 >> > > =A0Thanks=A0a=A0lot. >> > >=20 >> > > ?/DIV>=20 >> > >=20 >> > > =A0Best=A0regards, >> > >=20 >> > > ?/DIV>=20 >> > >=20 >> > > =A0Zhijian=A0Wu >> > >=20 Dear Dr. Zhijian Wu, =20 You have performed the steps I'd recommend, i.e. using the gas-phase Hessian or the Hessian from an Onsager calculation. Since these options did not work, it might be necessary to calculate the CPCM Hessian. You cannot do this with "opt=3D(ts,calcfc)" in G98, but you can perform a two-step job in which the first step uses "freq" and the second job step uses "opt=3D(ts,rcfc)". You might also consider performing an "opt=3Dqst3" calculation in which you use your Onsager model optimized TS as the initial guess structure for the CPCM transition state.=20 =20 =20 Regards, =20 Jim Hess =20 =20 On Thursday, April 24, 2003, at 01:13 AM, zjwu wrote: =20 =20 << excerpt> Dear Dr. Hess, =20 =20 ?/DIV>=20 =20 =20 I mean the job failing because the structure is not the TS structure anymore. The calculation may converge but goes to different geometry which I did not want. I have tried to read force constants at cpcm calculation from either gas phase frequency calculation or Onsager frequency calculation (these frequencies are obtained based on the optimized geometry) (calculation using Onsager model works well for the TS calculation).=A0In addition, I also tried opt=3D(ts,calcfc), but = as you know,=A0calcfc does not exist for=A0cpcm.=A0It seems g03 is = possible to calculate fc at cpcm level. =20 =20 ?/DIV>=20 =20 =20 Hope I have made myself clear. =20 =20 ?/DIV>=20 =20 =20 Thank you very much for your answer. =20 =20 ?/DIV>=20 =20 =20 Best regards, =20 =20 ?/DIV>=20 =20 =20 Zhijian Wu =20 =20 ?/DIV>=20 =20 =20 =20 =20 << /excerpt> < < image.tiff>=20 =20 << excerpt>=20 =20 Dear=A0Dr.=A0Zhijian=A0Wu, =20 =A0=A0=A0=A0Is=A0this=A0job=A0failing=A0because=A0it=A0runs=A0out=A0of=A0= optimization=A0cycles?=A0I 'd?/DIV>=20 =20 need=A0to=A0know=A0more=A0details=A0about=A0what=A0is=A0going=A0wrong=A0= before=A0I=A0make?/DIV>=20 =20 detailed=A0suggestions,=A0but=A0one=A0possible=A0way=A0to=A0improve=A0th= is=A0calculation?/DIV> =20 is=A0to=A0calculate=A0the=A0force=A0constants=A0in=A0the=A0solution=A0ph= ase,=A0then=A0use?/DIV>=20 =20 these=A0force=A0constants=A0to=A0start=A0the=A0transition=A0state=A0sear= ch..=A0Usually=A0t he?/DIV>=20 =20 gas-phase=A0Hessian=A0is=A0a=A0good=A0enough=A0approximation,=A0but=A0in= =A0some=A0cases?/DIV>=20 =20 where=A0the=A0gas-phase=A0and=A0solution-phase=A0potential=A0energy=A0su= rfaces=A0are?/DIV>=20 =20 different=A0enough,=A0explicitly=A0calculating=A0the=A0second=A0derivati= ves=A0in=A0the?/DIV> =20 solution=A0phase=A0can=A0be=A0helpful.=A0Incidentally,=A0if=A0you=A0are=A0= using=A0G98,=A0the?/DIV> =20 CPCM=A0second=A0derivatives=A0will=A0be=A0performed=A0by=A0numerical=A0d= ifferentiation?/DIV> =20 of=A0the=A0analytic=A0gradients=A0and=A0if=A0you=A0are=A0using=A0G03,=A0= the=A0second?/DIV>=20 =20 derivatives=A0will=A0be=A0calculated=A0analytically. =20 ?/DIV>=20 =20 Regards, =20 Jim=A0Hess =20 ?/DIV>=20 =20 ++++++++++++++++++++++++++ =20 James=A0Hess,=A0Ph.D. =20 Customer=A0Support=A0Scientist =20 Gaussian,=A0Inc. =20 e-mail:=A0help@gaussian.com =20 ++++++++++++++++++++++++++ =20 ?/DIV>=20 =20 ?/DIV>=20 =20 On=A0Tuesday,=A0April?2,?003,=A0at?8:29=A0PM,=A0zjwu=A0wrote: =20 ?/DIV>=20 =20 >> > =A0Dear=A0members, =20 >> >=20 =20 >> > ?/DIV>=20 =20 >> >=20 =20 >> > = =A0I=A0am=A0trying=A0to=A0locate=A0the=A0transition=A0state=A0using=A0cp= cm=A0model.=A0T he?/DIV>=20 =20 >> > = =A0initial=A0structure=A0is=A0from=A0gas=A0phase=A0optimized=A0transitio= n=A0s tructure?/DIV>=20 =20 >> >=20 ?with=A0correct=A0vibrational=A0mode).=A0The=A0optimization=A0at=A0cpcm=A0= level=A0fails?/DIV>=20 =20 >> > =A0by=A0the=A0following=A0keywords =20 >> >=20 =20 >> > ?/DIV>=20 =20 >> >=20 =20 >> >=20 ?b3lyp/6-31g(d,p)=A0opt=3D(ts,=A0readfc,=A0noeigen)=A0scrf=3D(cpcm,solve= nt=3Dwater) =20 >> >=20 =20 >> > ?/DIV>=20 =20 >> >=20 =20 >> > = =A0Do=A0anybody=A0has=A0experience=A0in=A0cpcm=A0transition=A0structure=A0= calculation? =20 >> >=20 =20 >> > ?/DIV>=20 =20 >> >=20 =20 >> > =A0Thanks=A0a=A0lot. =20 >> >=20 =20 >> > ?/DIV>=20 =20 >> >=20 =20 >> > =A0Best=A0regards, =20 >> >=20 =20 >> > ?/DIV>=20 =20 >> >=20 =20 >> > =A0Zhijian=A0Wu =20 >> >=20 =20 << /excerpt>=20 _____ =20 ------_=_NextPart_001_01C30D8B.7CFE4640 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Please=20 take a look at Wang, Nakamura, Balbuena, JACS, 2002, Vol. 124,=20 4408.
We had=20 used PCM-B3PW91 in the paper as well as CPCM (to be published)=20 to
optimize reductive decomposition TS = (page 4410,=20 structure 7) of vinylene carbonate.
 
Yixuan=20 Wang
 
Department of Chem. = Engineering
Univ.=20 South Carolina 
 
-----Original Message-----
From: zjwu=20 [mailto:zjwu@ns.ciac.jl.cn]
Sent: Thursday, May 01, 2003 = 8:27=20 PM
To: help@gaussian.com
Cc:=20 chemistry@ccl.net
Subject: CCL:Re: CPCM TS=20 location

Dear Dr. Hess,

 

Do you know any publications containing cpcm ts structure=20 calculations? I do find some papers on local minima optimizations = using cpcm,=20 but did not see any paper on transition state calculation using cpcm=20 model?

 

Any papers on this aspect are appreaciated.

 

Best wishes,

 

Zhijian Wu

Dear Dr. Zhijian Wu,
=
    You have performed the = steps I'd recommend, i.e. using the gas-ph= ase  
=
Hessian or the Hessian from an Onsage= r calculation. Since these options  
= =
did not work, it might be necessary&n= bsp;to calculate the CPCM Hessian. You &nb= sp;
=
cannot do this with "opt=3D(ts,calcfc)" in=  G98, but you can perform a   =
two-step job in which the first step&= nbsp;uses "freq" and the second job  =
=
step uses "opt=3D(ts,rcfc)". You might als= o consider performing an  
=
"opt=3Dqst3" calculation in which you use&= nbsp;your Onsager model optimized TS   =
as the initial guess structure for th= e CPCM transition state.
 
Regards,
Jim Hess
 
=
On Thursday, April 24, 2003, at 01:13=  AM, zjwu wrote:
 
>>  Dear Dr. Hess,
>>
>>  ?/DIV>=20
>>
>>=20 =  I mean the job failing because the&n= bsp;structure is not the TS structure &nbs= p;
>>=20 =  anymore. The calculation may converge but=  goes to different geometry  
>>=20 =  which I did not want. I have tr= ied to read force constants at cpcm &= nbsp;
>>=20 =  calculation from either gas phase frequen= cy calculation or Onsager  
>>=20 =  frequency calculation (these frequencies are&n= bsp;obtained based on the  
>>=20 =  optimized geometry) (calculation using Onsager=  model works well for  
>>=20 =  the TS calculation).=A0In addition, I als= o tried opt=3D(ts,calcfc), but as  
>>=20 =  you know,=A0calcfc does not exist for=A0c= pcm.=A0It seems g03 is possible to  <= /DIV>
>> =  calculate fc at cpcm level.
>>
>>  ?/DIV>=20
>>
>>=20  Hope I have made myself clear.
>>
>>  ?/DIV>=20
>>
>>=20 =  Thank you very much for your answer.=
>>
>>  ?/DIV>=20
>>
>>  Best regards,
>>
>>  ?/DIV>=20
>>
>>  Zhijian Wu
>>
>>  ?/DIV>=20
>>
>>
>>
<< image.tiff>
>>
>>  Dear=A0Dr.=A0Zhijian=A0Wu,
>>=20 =  =A0=A0=A0=A0Is=A0this=A0job=A0failing=A0because=A0it=A0runs=A0out=A0= of=A0optimization=A0cycles?=A0I'd 
>>  ?/DIV>=20
>>=20 =  need=A0to=A0know=A0more=A0details=A0about=A0what=A0is=A0going=A0wr= ong=A0before=A0I=A0make?/DIV>=20
>>=20 =  detailed=A0suggestions,=A0but=A0one=A0possible=A0way=A0to=A0improv= e=A0this=A0calculation?/DIV>=20
>>=20 =  is=A0to=A0calculate=A0the=A0force=A0constants=A0in=A0the=A0solutio= n=A0phase,=A0then=A0use?/DIV>=20
>>=20 =  these=A0force=A0constants=A0to=A0start=A0the=A0transition=A0state=A0= search.>.=A0Usually=A0the 
>>  ?/DIV>=20
>>=20 =  gas-phase=A0Hessian=A0is=A0a=A0good=A0enough=A0approximation,=A0bu= t=A0in=A0some=A0cases?/DIV>=20
>>=20 =  where=A0the=A0gas-phase=A0and=A0solution-phase=A0potential=A0energ= y=A0surfaces=A0are?/DIV>=20
>>=20 =  different=A0enough,=A0explicitly=A0calculating=A0the=A0second=A0de= rivatives=A0in=A0the?/DIV>=20
>>=20 =  solution=A0phase=A0can=A0be=A0helpful.=A0Incidentally,=A0if=A0you=A0= are=A0using=A0G98,=A0the?/DIV>=20
>>=20 =  CPCM=A0second=A0derivatives=A0will=A0be=A0performed=A0by=A0numeric= al=A0differentiation?/DIV>=20
>>=20 =  of=A0the=A0analytic=A0gradients=A0and=A0if=A0you=A0are=A0using=A0G= 03,=A0the=A0second?/DIV>=20
>> =  derivatives=A0will=A0be=A0calculated=A0analytically.
>>  ?/DIV>=20
>>  Regards,
>>  Jim=A0Hess
>>  ?/DIV>=20
>>  ++++++++++++++++++++++++++
>>  James=A0Hess,=A0Ph.D.
>>  Customer=A0Support=A0Scientist
>>  Gaussian,=A0Inc.
>>  e-mail:=A0help@gaussian.com
>>  ++++++++++++++++++++++++++
>>  ?/DIV>=20
>>  ?/DIV>=20
>> =  On=A0Tuesday,=A0April?2,?003,=A0at?8:29=A0PM,=A0zjwu=A0wrote:
>>  ?/DIV>=20
>>  > >  =A0Dear=A0members,
>>  > >
>>  > >  ?/DIV>
>>  > >
>>  > >=20 =  =A0I=A0am=A0trying=A0to=A0locate=A0the=A0transition=A0state=A0usin= g=A0cpcm=A0model.=A0The?/DIV>=20
>>  > >=20 =  =A0initial=A0structure=A0is=A0from=A0gas=A0phase=A0optimized=A0tra= nsition=A0structure?/DIV>=20
>>  > >   
>>=20 =  ?with=A0correct=A0vibrational=A0mode).=A0The=A0optimization=A0at=A0= cpcm=A0level=A0fails?/DIV>=20
>>  > > =  =A0by=A0the=A0following=A0keywords
>>  > >
>>  > >  ?/DIV>
>>  > >
>>  > >   
>>=20 =  ?b3lyp/6-31g(d,p)=A0opt=3D(ts,=A0readfc,=A0noeigen)=A0scrf=3D(cpcm= ,solvent=3Dwater)
>>  > >
>>  > >  ?/DIV>
>>  > >
>>  > >=20 =  =A0Do=A0anybody=A0has=A0experience=A0in=A0cpcm=A0transition=A0stru= cture=A0calculation?
>>  > >
>>  > >  ?/DIV>
>>  > >
>>  > >  =A0Thanks=A0a=A0lot.
>>  > >
>>  > >  ?/DIV>
>>  > >
>>  > >  =A0Best=A0regards,
>>  > >
>>  > >  ?/DIV>
>>  > >
>>  > >  =A0Zhijian=A0Wu
>>  > >
Dear Dr. Zhijian Wu,
 
=
   You have performed the steps&= nbsp;I'd recommend, i.e. using the
=
gas-phase Hessian or the Hessian from = ;an Onsager calculation. Since
=
these options did not work, it might&= nbsp;be necessary to calculate the
=
CPCM Hessian. You cannot do this with=  "opt=3D(ts,calcfc)" in G98, but
=
you can perform a two-step job in&nbs= p;which the first step uses "freq" and =
the second job step uses "opt=3D(ts,rcfc)"= . You might also consider
=
performing an "opt=3Dqst3" calculation in = which you use your Onsager
=
model optimized TS as the initial gue= ss structure for the CPCM
transition state. 
 
 
Regards,
 
Jim Hess
 
 
=
On Thursday, April 24, 2003, at 01:13=  AM, zjwu wrote:
 
 
<< excerpt> Dear Dr. Hess,
 
 
?/DIV>=20
 
 
=
I mean the job failing because the&nb= sp;structure is not the TS structure
=
anymore. The calculation may converge but&= nbsp;goes to different geometry
=
which I did not want. I have tri= ed to read force constants at cpcm
=
calculation from either gas phase frequenc= y calculation or Onsager
=
frequency calculation (these frequencies are&nb= sp;obtained based on the
=
optimized geometry) (calculation using Onsager&= nbsp;model works well for
=
the TS calculation).=A0In addition, I also=  tried opt=3D(ts,calcfc), but as
=
you know,=A0calcfc does not exist for=A0cp= cm.=A0It seems g03 is possible to
calculate fc at cpcm level.
 
 
?/DIV>=20
 
 
Hope I have made myself clear.
 
 
?/DIV>=20
 
 
=
Thank you very much for your answer.<= /DIV>
 
 
?/DIV>=20
 
 
Best regards,
 
 
?/DIV>=20
 
 
Zhijian Wu
 
 
?/DIV>=20
 
 
 
 
<< /excerpt> < < image.tiff>
 
<< excerpt>
 
Dear=A0Dr.=A0Zhijian=A0Wu,
 
=
=A0=A0=A0=A0Is=A0this=A0job=A0failing=A0because=A0it=A0runs=A0out=A0= of=A0optimization=A0cycles?=A0I'd?/DIV>=20
 
=
need=A0to=A0know=A0more=A0details=A0about=A0what=A0is=A0going=A0wro= ng=A0before=A0I=A0make?/DIV>=20
 
=
detailed=A0suggestions,=A0but=A0one=A0possible=A0way=A0to=A0improve= =A0this=A0calculation?/DIV>=20
 
=
is=A0to=A0calculate=A0the=A0force=A0constants=A0in=A0the=A0solution= =A0phase,=A0then=A0use?/DIV>=20
 
=
these=A0force=A0constants=A0to=A0start=A0the=A0transition=A0state=A0= search..=A0Usually=A0the?/DIV>=20
 
=
gas-phase=A0Hessian=A0is=A0a=A0good=A0enough=A0approximation,=A0but= =A0in=A0some=A0cases?/DIV>=20
 
=
where=A0the=A0gas-phase=A0and=A0solution-phase=A0potential=A0energy= =A0surfaces=A0are?/DIV>=20
 
=
different=A0enough,=A0explicitly=A0calculating=A0the=A0second=A0der= ivatives=A0in=A0the?/DIV>=20
 
=
solution=A0phase=A0can=A0be=A0helpful.=A0Incidentally,=A0if=A0you=A0= are=A0using=A0G98,=A0the?/DIV>=20
 
=
CPCM=A0second=A0derivatives=A0will=A0be=A0performed=A0by=A0numerica= l=A0differentiation?/DIV>=20
 
=
of=A0the=A0analytic=A0gradients=A0and=A0if=A0you=A0are=A0using=A0G0= 3,=A0the=A0second?/DIV>=20
 
derivatives=A0will=A0be=A0calculated=A0analytically.
 
?/DIV>=20
 
Regards,
 
Jim=A0Hess
 
?/DIV>=20
 
++++++++++++++++++++++++++
 
James=A0Hess,=A0Ph.D.
 
Customer=A0Support=A0Scientist
 
Gaussian,=A0Inc.
 
e-mail:=A0help@gaussian.com
 
++++++++++++++++++++++++++
 
?/DIV>=20
 
?/DIV>=20
 
=
On=A0Tuesday,=A0April?2,?003,=A0at?8:29=A0PM,=A0zjwu=A0wrote:
=
 
?/DIV>=20
 
>> >  =A0Dear=A0members,
 
>> >
 
>> >  ?/DIV>
 
>> >
 
>> >=20 =  =A0I=A0am=A0trying=A0to=A0locate=A0the=A0transition=A0state=A0usin= g=A0cpcm=A0model.=A0The?/DIV>=20
 
>> >=20 =  =A0initial=A0structure=A0is=A0from=A0gas=A0phase=A0optimized=A0tra= nsition=A0structure?/DIV>=20
 
>> >
=
?with=A0correct=A0vibrational=A0mode).=A0The=A0optimization=A0at=A0= cpcm=A0level=A0fails?/DIV>=20
 
>> >  =A0by=A0the=A0following=A0keywords
 
>> >
 
>> >  ?/DIV>
 
>> >
 
>> >
=
?b3lyp/6-31g(d,p)=A0opt=3D(ts,=A0readfc,=A0noeigen)=A0scrf=3D(cpcm,= solvent=3Dwater)
 
>> >
 
>> >  ?/DIV>
 
>> >
 
>> >=20 =  =A0Do=A0anybody=A0has=A0experience=A0in=A0cpcm=A0transition=A0stru= cture=A0calculation?
 
>> >
 
>> >  ?/DIV>
 
>> >
 
>> >  =A0Thanks=A0a=A0lot.
 
>> >
 
>> >  ?/DIV>
 
>> >
 
>> >  =A0Best=A0regards,
 
>> >
 
>> >  ?/DIV>
 
>> >
 
>> >  =A0Zhijian=A0Wu
 
>> >
 
<< /excerpt>
=
=
=
=
=
------_=_NextPart_001_01C30D8B.7CFE4640-- From chemistry-request@server.ccl.net Mon Apr 28 13:12:40 2003 Received: from magnum.cooper.edu ([199.98.16.4]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3SHCdo12655 for ; Mon, 28 Apr 2003 13:12:40 -0400 Received: from robin.cooper.edu by magnum.cooper.edu with SMTP id AA15055 (5.65c/IDA-1.4.4 for ); Mon, 28 Apr 2003 13:16:44 -0400 Received: from localhost by robin.cooper.edu (SMI-8.6/SMI-SVR4) id NAA24679; Mon, 28 Apr 2003 13:12:37 -0400 Date: Mon, 28 Apr 2003 13:12:37 -0400 (EDT) From: "kulik@cooper.edu" To: chemistry@ccl.net Subject: Spartan 5.2 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am an undergraduate student, and I am not very familiar with computational chemistry, so excuse me if my question appears stupid. I have been running some conformational searches using Spartan 5.1 and then I switched over to Spartan 5.2 to complete the same searches on the same molecule (a pyridine carboxamide). In some instances Spartan 5.2 conformers included the remark "Rejected No Minima" which would imply that the search failed, I guess. However, the results of the 5.2 and 5.1 searches match fairly well. That is, the absolute energy of the lowest energy conformer varies by .25 kcal/mol but the relative energies of the various conformers exhibit the same pattern and they appear to predict the same dihedrals. Is the Spartan 5.2 search failing? Has anyone had any experience with Spartan 5.2? Thanks for your time. Heather Kulik From chemistry-request@server.ccl.net Tue Apr 29 05:08:11 2003 Received: from smtp03.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3T984o00890 for ; Tue, 29 Apr 2003 05:08:08 -0400 Received: from lq (unknown [202.127.145.3]) by smtp03.sohu.com (Postfix) with ESMTP id 67C6C58FB for ; Tue, 29 Apr 2003 17:07:55 +0800 (CST) From: "Li Qiang" To: "chemistry@ccl.net" Subject: SARS drug design X-mailer: Foxmail 4.2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Date: Mon, 29 Apr 2002 17:7:43 +0800 Message-Id: <20030429090755.67C6C58FB@smtp03.sohu.com> Dear CCLers, Do you know the SARS, Can you discuss with us about the SARS drug design? How to get structure from the RNA sequences? Thank you for advance ! cola From chemistry-request@server.ccl.net Mon Apr 28 17:21:53 2003 Received: from cbdcom-emh1.apgea.army.mil ([131.92.10.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3SLLro08417 for ; Mon, 28 Apr 2003 17:21:53 -0400 Received: by cbdcom-emh1.apgea.army.mil with Internet Mail Service (5.5.2656.59) id ; Mon, 28 Apr 2003 17:21:52 -0400 Message-ID: <876D38F61109514A85ACA5772B7B07BB02D549AE@mail1.apgea.army.mil> From: "Balboa, Alex Dr. SBCCOM" To: "'chemistry@ccl.net'" Subject: updated scaling factors for calculated vibrational frequencies Date: Mon, 28 Apr 2003 17:21:47 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C30DCB.AAD93FD4" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C30DCB.AAD93FD4 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I was wondering if there is any updated journal article/site that have scaling factors for calculated vibrational frequencies (the latest = article seems to be: Harmonic Vibrational Frequencies: An Evaluation of Hartree-Fock, M=F8ller-Plesset, Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors Anthony P. Scott and Leo Radom* Research School of Chemistry, Australian National UniVersity, Canberra, = ACT 0200, Australia ReceiVed: April 2, 1996; In Final Form: July 30, 1996X J. Phys. Chem. 1996, 100, 16502-16513 I am particularly interested in B3LYP/6-31G**. Any feedback or reply = would be greatly appreciated. Thanks in advance. Sincerely, Alex Balboa Chemist US Army Soldier Biological, Chemical Command Chem-Bio Radiological Filtration Team Tech Dir, ECBC ATTN: AMSSB-RRT-PF Bldg E3549, Section C500, Cubicle 115 5183 Blackhawk Road Aberdeen Proving Ground-Edgewood Area, MD 21010-5424 Telephone: (410)436-5913 FAX: (410)436-7695 email: axbalboa@sbccom.apgea.army.mil ------_=_NextPart_001_01C30DCB.AAD93FD4 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable updated scaling factors for calculated vibrational = frequencies

Hi,
I was wondering if there is any = updated journal article/site that have scaling factors for calculated = vibrational frequencies (the latest article seems to be:

Harmonic Vibrational = Frequencies: An Evaluation of Hartree-Fock, M=F8ller-Plesset,
Quadratic Configuration = Interaction, Density Functional Theory, and Semiempirical = Scale
Factors
Anthony P. Scott and Leo = Radom*
Research School of = Chemistry, Australian National UniVersity, Canberra, ACT 0200, Australia
ReceiVed: April 2, 1996; In Final Form: July 30, = 1996X
J. Phys. = Chem. 1996, 100, 16502-16513

I am particularly interested in = B3LYP/6-31G**.  Any feedback or reply would be greatly = appreciated.

Thanks in advance.
Sincerely,
Alex Balboa
Chemist
US Army Soldier Biological, Chemical = Command
Chem-Bio Radiological Filtration = Team
Tech Dir, ECBC
ATTN:  AMSSB-RRT-PF
Bldg E3549, Section C500, Cubicle = 115
5183 Blackhawk Road
Aberdeen Proving Ground-Edgewood = Area, MD  21010-5424
Telephone: (410)436-5913
FAX: (410)436-7695
email: = axbalboa@sbccom.apgea.army.mil

------_=_NextPart_001_01C30DCB.AAD93FD4-- From chemistry-request@server.ccl.net Tue Apr 29 07:24:36 2003 Received: from kuzey.cc.boun.edu.tr ([193.140.192.30]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3TBOWo14371 for ; Tue, 29 Apr 2003 07:24:34 -0400 Received: (qmail 80087 invoked from network); 29 Apr 2003 12:22:41 -0000 Received: from unknown (HELO kennedy.cc.boun.edu.tr) (193.140.192.10) by 0 with SMTP; 29 Apr 2003 12:22:41 -0000 Received: from saritepe.cc.boun.edu.tr ([193.140.192.31]) by kennedy.cc.boun.edu.tr (SAVSMTP 3.0.0.44) with SMTP id M2003042914251203558 for ; Tue, 29 Apr 2003 14:25:12 +0300 Received: (qmail 7336 invoked by uid 80); 29 Apr 2003 14:26:46 -0000 Received: from 212.252.6.204 ([212.252.6.204]) by webmail.boun.edu.tr (IMP) with HTTP for ; Tue, 29 Apr 2003 14:26:46 +0000 Message-ID: <1051626406.3eae8ba6a733f@webmail.boun.edu.tr> Date: Tue, 29 Apr 2003 14:26:46 +0000 From: sungura@boun.edu.tr To: chemistry@ccl.net Subject: error in iefpcm MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 Dear CCLers I have a problem with iefpcm ts optimization. The calculations have done at b3lyp/6-31g* level and g98 gave me an error like 16 16 1.200 1.200 17 17 1.200 1.200 18 18 1.200 1.200 19 19 1.200 1.200 20 20 1.200 1.200 ------------------------------------------------------------------------------- Too many tesserae in PolyGen Error termination via Lnk1e in /usr/local/g98/l502.exe. Job cpu time: 0 days 0 hours 1 minutes 21.9 seconds. File lengths (MBytes): RWF= 79 Int= 0 D2E= 0 Chk= 7 Scr= 1 the additional keywords are noscfvac nocav tsare=0.001 radii=bondi alpha=1.2 alphaH=1.2 Although I have changed the tsare number to 0.4. This time optimization cannot completed due to - Number of steps exceeded, NStep= 99 -- Flag reset to prevent archiving. error Does anyone know how to solve this problem thanks in advance aylin. From chemistry-request@server.ccl.net Mon Apr 28 14:07:12 2003 Received: from sentry.ucr.edu ([138.23.226.224]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3SI7Co18907 for ; Mon, 28 Apr 2003 14:07:12 -0400 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentry.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id AKC47535 for ; Mon, 28 Apr 2003 11:07:11 -0700 (PDT) Reply-To: From: "Donald Keidel" To: Subject: CCL: SUMMARY: Software to animate frequency calc Date: Mon, 28 Apr 2003 11:07:07 -0700 Organization: UCR Message-ID: <000001c30db0$fb425760$529c178a@dopetec> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C30D76.4EE37F60" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C30D76.4EE37F60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, =20 I want to thank everyone who responded to my request for information. All responses were very helpful. Thank you all again. =20 =20 I think Molden can do this as a series of gifs. =20 -Cory=20 =20 =20 =20 "Molden" (available for nearly all platforsm, although UNIX is supported best) can read g98-outputs and animate the frequencies. A movie can't be saved, as far as I remember.... =20 but =20 xmakemol and xvibs together are nearly perfect: =20 xvibs extracts the normal modes from a g98 output (avbailable as src code, infos in the header) and puts them in *.xyz files,=20 that can be read from (beside molden and much other programs) by xmakemol (LINUX tool, available as src, bin, rpm, deb,...), which has the possibility to save animations. It creates *.xpm files, which=20 can be concatenated together to become an mpeg or animated gif file. I guess the "Help" function or webpage woll tell more.... =20 All software is best found by a www search with e.g. "www.google.com". =20 If you can't find something, let me know and I'll help you. =20 =20 Bye Elmar =20 =20 I use molekel to create rendered frames from g98 output, and then some=20 sgi tools to convert them into a movie.=20 The molekel people have done the same thing here: http://www.cscs.ch/molekel/gallery.html =20 You could probably find free tools or write scripts to catenate and=20 convert from image frames to a movie format if you don't have this=20 already; here for example: http://www.gnu.org/directory/graphics/anim/ Or by screen capture while molekel is playing:=20 http://www.gnu.org/directory/vid/ =20 Molekel has a reputation for beautiful rendering and ease of use. If you find a handier or more attractive solution, please let me know. =20 Hope this helps, =20 Jeremy =20 Hi, =20 I have used Jmol=20 =20 http://jmol.sourceforge.net/ =20 to visualize vibrational motion. =20 Best regards, =20 Per-Olof =C5strand =20 =20 Molden can animate frecuencies and you can save and view them via the opengl utility moldenogl. Sometimes it results in weird molecules with unbelievable bonds, but, when it works well, the result is pretty good. =20 _-_-_-_-_-_-_-_-_-_-_-_- =20 Carlos Silva L=F3pez =20 =20 Dear Don, Maybe molden is not a very fancy program, but it is quite a good help when calculating with gaussian (and it is free!). If you have it, you can enter the program and use the second button from the top (it looks like a photographic camera). This command creates one gif file each time the frame being displayed changes, so just animate the vibration ("normal mode" button) click this button and wait for a while (just don't forget to click this button again, if you don't want to completely fill your disk!). Then, you can make an animated .gif with any graphic program (photoshop...). Another way (smarter) of doing this is to open molden with the command: =20 "molden -w 1" and animate the normal mode you want. Then, you open again with molden the file "freq.dat" that was created in the previous step, click the camera button and animate the sequence with "movie". Then, you exit the program and process the *.gif files thus obtained. =20 Hope it helps. Regards =20 =20 =20 Olalla Nieto Faza =20 =20 Try gOpenMol =20 http://www.csc.fi/gopenmol/ =20 Jim =20 =20 Hi Don =20 I know exactly the problem you're having, I had the same thing myself last year. I use gOpenMol http://www.csc.fi/gopenmol/ - it isn't the easiest thing in the world to learn to use, but if you download the manual (I can't attach it as it is 10Mb) then look at page 203 for the animation instructions. In fact the whole of app. 5 (starts on page 195) is what I use all the time. I found that I had to use the stand alone version of xvibs. If you download it and install it and then can't figure out how to get it to work then let me know and I'll try to write out how I do it for animations of vibrations. I guess that you're wanting to have them in talks - the mpeg is usually under 200kb in size so it is really good. =20 Hope this is of help to you =20 Roma =20 =20 Hi, =20 to animate frequencies we use molden. But for recording the video to play it in presentations we found is useful to use HyperCam (not HyperChem of course!). This is a general screen-recorder like a screen capture tool which recorders videos with up to 15 frames per second (I think). If your machine is fast enough (pentium 600) to animate the frequencies and record them at the same time you will get a standard avi file which can be edited with any video editing software. =20 Regards =20 Eike Huebner =20 =20 HyperChem with HyperCam should be able to do this from a checkpoint file. I think you can save it as an *.avi file to input into PowerPoint. I did this a couple of years ago with a simple CO2 mode. The movie is not=20 great quality, but the graphics were acceptable. =20 James Kubicki =20 =20 ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec@dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm =20 =20 ------=_NextPart_000_0001_01C30D76.4EE37F60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello all,

 

I want to thank everyone who responded to my request = for information.=A0 All responses were very helpful.=A0 Thank you all = again.

 

=A0

I think Molden can = do this as a series of gifs.

 

-Cory =

 

=A0=A0 =

 

"Molden" (available for nearly all platforsm, although UNIX is supported best) = can read g98-outputs and animate the frequencies. A movie can't be saved, as far = as I remember....

 

but

 

xmakemol and xvibs = together are nearly perfect:

 

xvibs extracts = the=A0 normal modes from a g98 output

(avbailable as src = code, infos in the header) and puts them in *.xyz files,

that can be read = > from (beside molden and much other programs) by xmakemol (LINUX tool, = available as src, bin, rpm, deb,...), which has the possibility to save animations. It = creates *.xpm files, which

can be concatenated = together to become an mpeg or animated gif file. I guess the "Help" = function or webpage woll tell more....

 

All software is = best found by a www search with e.g. "www.google.com".

 

If you can't find = something, let me know and I'll help you.

 

 

Bye

Elmar

 

 

I use molekel to = create rendered frames from g98 output, and then some

sgi tools to = convert them into a movie.

The molekel people = have done the same thing here: http://www.cscs.ch/molek= el/gallery.html

 

You could probably = find free tools or write scripts to catenate and

convert from image = frames to a movie format if you don't have this

already; here for = example: http://www.gnu.org/d= irectory/graphics/anim/

Or by screen = capture while molekel is playing:

http://www.gnu.org/directory/v= id/

 

Molekel has a = reputation for beautiful rendering and ease of use. If you find a handier or more = attractive solution, please let me know.

 

Hope this = helps,

 

Jeremy

 

Hi,

 

I have used Jmol =

 

http://jmol.sourceforge.net/

 

to visualize = vibrational motion.

 

Best = regards,

 

Per-Olof = =C5strand

 

 

Molden can animate = frecuencies and you can save and view them via the opengl utility moldenogl. = Sometimes it results in weird molecules with unbelievable bonds, but, when it works = well, the result is pretty good.

 

_-_-_-_-_-_-_-_-_-_-_-_-

 

=A0=A0 Carlos Silva = L=F3pez

 

 

Dear = Don,

Maybe molden is not = a very fancy program, but it is quite a good help when calculating with = gaussian (and it is free!). If you have it, you can enter the program and use the = second button from the top (it looks like a photographic camera). This command = creates one gif file each time the frame being displayed changes, so just = animate the vibration ("normal mode" button) click this button and wait = for a while (just don't forget to click this button again, if you don't want = to completely fill your disk!). Then, you can make an animated .gif with = any graphic program (photoshop...). Another way (smarter) of doing this is = to open molden with the command:

 

"molden -w = 1" and animate the normal mode you want. Then, you open again with molden the = file "freq.dat" that was created in the previous step, click the = camera button and animate the sequence with "movie". Then, you exit = the program and process the *.gif files thus obtained.

 

Hope it = helps.

Regards

 

 

 

Olalla Nieto = Faza

 

 

Try = gOpenMol

 

http://www.csc.fi/gopenmol/

 

Jim

 

 

Hi = Don

 

I know exactly the = problem you're having, I had the same thing myself last year. I use gOpenMol http://www.csc.fi/gopenmol/ - = it isn't the easiest thing in the world to learn to use, but if you download the = manual (I can't attach it as it is 10Mb) then look at page 203 for the = animation instructions. In fact the whole of app. 5 (starts on page 195) is what I = use all the time. I found that I had to use the stand alone version of = xvibs. If you download it and install it and then can't figure out how to get it = to work then let me know and I'll try to write out how I do it for animations of vibrations. I guess that you're wanting to have them in talks - the mpeg = is usually under 200kb in size so it is really good.

 

Hope this is of = help to you

 

Roma

 

 

Hi,

 

to animate = frequencies we use molden. But for recording the video to play it in presentations we = found is useful to use HyperCam (not HyperChem of course!). This is a general screen-recorder like a screen capture tool which recorders videos with = up to 15 frames per second (I think). If your machine is fast enough (pentium = 600) to animate the frequencies and record them at the same time you will get a standard avi file which can be edited with any video editing = software.

 

Regards

 

Eike = Huebner

 

 

HyperChem with = HyperCam should be able to do this from a checkpoint file. I think you can save = it as an *.avi file to input into PowerPoint. I did this a couple of years ago = with a simple CO2 mode.=A0 The movie is not

great quality, but = the graphics were acceptable.

 

James Kubicki

 

 

------------------------------------------------------= ---------------------------------------------------------
Donald J. Keidel
University of California, Riverside
Department of Biochemistry and Molecular Biology
Riverside, CA = 92521
phone:  (909) 787-5493
fax:  (909) 787-4434
dopetec@dslextreme.com
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /span>

 

 

------=_NextPart_000_0001_01C30D76.4EE37F60-- From chemistry-request@server.ccl.net Tue Apr 29 10:31:04 2003 Received: from llar.net.uniovi.es ([156.35.11.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TEUio20089 for ; Tue, 29 Apr 2003 10:31:03 -0400 Received: from CONVERSION-DAEMON.llar.net.uniovi.es by llar.net.uniovi.es (PMDF V6.1 #39514) id <01KVB19B11LS003KHN@llar.net.uniovi.es> for chemistry@ccl.net; Tue, 29 Apr 2003 16:30:26 +0200 (MET) Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by llar.net.uniovi.es (PMDF V6.1 #39514) with ESMTP id <01KVB199DZWE003FHF@llar.net.uniovi.es>; Tue, 29 Apr 2003 16:30:24 +0200 (MET) Received: from pinon.ccu.uniovi.es (localhost [127.0.0.1]) by pinon.ccu.uniovi.es (8.12.9/8.12.9) with ESMTP id h3TEULn9020297; Tue, 29 Apr 2003 16:30:22 +0200 (METDST) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.12.9/8.12.8/Submit) id h3TEUKm2020296; Tue, 29 Apr 2003 16:30:20 +0200 (METDST) Date: Tue, 29 Apr 2003 16:30:20 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:Slater basis sets To: chemistry@ccl.net, owner-chemistry@server.ccl.net Message-id: <200304291430.h3TEUKm2020296@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT > From: Richard Muller > I'm doing some QMC calculations in which I would like to use Slater > (rather than Gaussian) basis sets. Can anyone recommend a good > reference for STO basis sets of different quality? I have the STO basis > sets that were used for the STO-NG (which can be found in Hehre, > Stewart, Pople JCP 51,2657 (1969), and Hehre, Ditchfield, Stewart, > Pople JCP 52, 2769 (1970)), but I don't have any others. Can any of the > CCLers out there point me to a good place to look? Thanks in advance. Koga et al have systematically improved the classical STO basis sets by Clementi-Roetti, McLean, etc. Look for the bases and references in A. J. Thakkar's web page. Particularly: http://www.unb.ca/chem/ajit/f_download.htm Regards, Victor Lua~na From chemistry-request@server.ccl.net Tue Apr 29 11:04:00 2003 Received: from webmail.mta.ca ([138.73.1.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TF40o21000 for ; Tue, 29 Apr 2003 11:04:00 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.04) id 19AWfL-0003WK-00 for chemistry@ccl.net; Tue, 29 Apr 2003 12:05:07 -0300 Received: from 138.73.24.166 ( [138.73.24.166]) as user srwhttl@mailserv.mta.ca by webmail.mta.ca with HTTP; Tue, 29 Apr 2003 12:05:07 -0300 Message-ID: <1051628707.3eae94a315256@webmail.mta.ca> Date: Tue, 29 Apr 2003 12:05:07 -0300 From: srwhttl@mta.ca To: chemistry@ccl.net Subject: Accuracy of Semi-empirical Eigenvalues MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.166 I am trying to find out the accuracy of semi-empirical Eigenvalues. Specifically, what is the number of decimal places that should be reported? Any feedback would be gratefully appreciated. Thanks, Sarah Whittleton Mount Allison University, Canada srwhttl@mta.ca From chemistry-request@server.ccl.net Tue Apr 29 10:05:31 2003 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TE5Uo19278 for ; Tue, 29 Apr 2003 10:05:30 -0400 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id QAA26842; Tue, 29 Apr 2003 16:03:59 +0200 (MEST) for From: cbiot@ulb.ac.be Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id QAA18460; Tue, 29 Apr 2003 16:05:24 +0200 (MET DST) for Message-ID: <3EAEA32F.3000203@ulb.ac.be> Date: Tue, 29 Apr 2003 16:07:11 +0000 Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: fr, en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: vibrational frequencies and potential energy surface X-Priority: 1 (highest) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3TE5Vo19279 Dear all, I am looking for bibliographic references dealing with vibrational frequencies and potential energy surface. Could the frequencies be calculated for each point of the surface or only at a minimum? Any reply would be greatly appreciated. Thanks in advance. CB -- ******************************************************** Dr. BIOT Christophe Ingénierie Moléculaire et Biomoléculaire, CP 165/64 Université Libre de Bruxelles 50 Av. F.D. Roosevelt 1050 Bruxelles, BELGIQUE Phone: 32-2-650 3001 Fax: 32-2-650 3606 E-mail:cbiot@ulb.ac.be http://babylone.ulb.ac.be/~christophe/ ******************************************************** From chemistry-request@server.ccl.net Tue Apr 29 10:31:05 2003 Received: from mailserv.unb.ca ([131.202.3.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TEV5o20108 for ; Tue, 29 Apr 2003 10:31:05 -0400 Received: from pop.unb.ca (root@newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h3TEV40W022816 for ; Tue, 29 Apr 2003 11:31:04 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.11.7+Sun/8.11.7) with ESMTP id h3TEV3d04454 for ; Tue, 29 Apr 2003 11:31:03 -0300 (ADT) X-WebMail-UserID: s808o Date: Tue, 29 Apr 2003 11:31:03 -0300 Sender: Joey Harriman From: Joey Harriman To: chemistry@ccl.net X-EXP32-SerialNo: 00003025, 00003442 Subject: Gaussian98 question Message-ID: <3EB137B9@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: Hi, I am trying to do a geometry optimization in Gaussian 98 on an organic salt. I am using a N3 azide (ionized) and a imidazolium salt (ionized). To date I have done the following: 1. Found a crystal packing structure of a very similar azide salt. 2. Recreated the packing scheme with my molecules in MOE (roughly the same distance and orientation between molecules) and saved this as a PDB file. 3. I converted the PDB into a new Zmap in Gaussian and did the optimization at the HF/STO-3G level. This is where my results become weird. The resulting optimized structure has formed a nonsensical covalent bond to the imidazolium ring. Any suggestions? Is there a specific way to treat salts in G98W? Any help would be greatly appreciated. Thanks, Joey Harriman ---------------------------------- Joey Harriman MSc Computational Chemistry Toole Hall Room 228 Dept. of Chemistry University of New Brunswick Bag Service # 45222 E3B 6E2 454-1173 or 449-2543 ---------------------------------- From chemistry-request@server.ccl.net Tue Apr 29 10:45:07 2003 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TEj6o20642 for ; Tue, 29 Apr 2003 10:45:06 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Tue, 29 Apr 2003 11:52:41 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B1F@correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: freqmem utility in g98w Date: Tue, 29 Apr 2003 11:52:36 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3TEj7o20643 Dear CCLers, I'm using g98w revision A-9. The manual describes a utility program called freqmem which I would like to use. But it is not on the original CD I have. Does anyone know if it comes with this revision? Does any know where I might be able to download a copy. I have asked the boys at Gaussian but have had no reply. Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Ciência e da Tecnologia- MCT Avenida Ipê, No 900 - Cidade Universitaria Ilha do Fundão Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell@cetem.gov.br From chemistry-request@server.ccl.net Tue Apr 29 11:20:17 2003 Received: from antivirus2.its.rochester.edu ([128.151.57.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TFKHo21621 for ; Tue, 29 Apr 2003 11:20:17 -0400 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h3TFKHF1020535 for ; Tue, 29 Apr 2003 11:20:17 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with SMTP id h3TFKGTp020529; Tue, 29 Apr 2003 11:20:16 -0400 (EDT) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.9/8.12.1) with ESMTP id h3TFKFHD010797; Tue, 29 Apr 2003 11:20:15 -0400 (EDT) Content-Type: text/plain; charset="iso-8859-1" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: NAMD Support Subject: help about NAMD Date: Tue, 29 Apr 2003 11:19:28 -0400 User-Agent: KMail/1.4.1 References: In-Reply-To: Cc: chemistry@ccl.net MIME-Version: 1.0 Message-Id: <200304291119.28539.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3TFKHo21622 Dear Sir: In my simulation, I want to fix the bond length of a molecule ( not only the bonds include H atoms) in order to do the vibrational analysis. I know that in charmm I can use shake to do it. but in NAMD seems like shake can only fix the bonds involve H atoms. is it right? if so, what can I use in NAMD to do this thing. Best Regards Wei Zhuang From chemistry-request@server.ccl.net Tue Apr 29 11:20:38 2003 Received: from llar.net.uniovi.es ([156.35.11.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TFKbo21648; Tue, 29 Apr 2003 11:20:37 -0400 Received: from CONVERSION-DAEMON.llar.net.uniovi.es by llar.net.uniovi.es (PMDF V6.1 #39514) id <01KVB2ZUO2PS003LCL@llar.net.uniovi.es>; Tue, 29 Apr 2003 17:20:08 +0200 (MET) Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by llar.net.uniovi.es (PMDF V6.1 #39514) with ESMTP id <01KVB2ZRC77I003HAN@llar.net.uniovi.es>; Tue, 29 Apr 2003 17:20:01 +0200 (MET) Received: from pinon.ccu.uniovi.es (localhost [127.0.0.1]) by pinon.ccu.uniovi.es (8.12.9/8.12.9) with ESMTP id h3TFJwn9021313; Tue, 29 Apr 2003 17:19:59 +0200 (METDST) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.12.9/8.12.8/Submit) id h3TFJv4k021312; Tue, 29 Apr 2003 17:19:57 +0200 (METDST) Date: Tue, 29 Apr 2003 17:19:57 +0200 (METDST) From: Victor Lua~na Subject: Re: CCL:how to 'protect' point charges in Gaussian? To: CHEMISTRY@server.ccl.net, owner-chemistry@server.ccl.net Message-id: <200304291519.h3TFJv4k021312@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT > From: David Price > I am trying to set up a calculation that has an oxide cluster > surrounded by point charges, but want to restrict the ability of the > oxide ions to polarise to much towards the positive point charges. > The point charges are included to mimic other ions in a lattice and thus > even the positive charges will repel the electron gas cloud of the oxide > ions at some distance from the point charge corresponding to the > positive > ion's 'radius'. How do I do this in Gaussian? I thought of using > pseudo-potentials centred on the positive point charges, but wasn't sure > if I could get one the right shape. Dave, Perhaps you can find the next reference useful for your purpose. @article{ov-LR2001, author = { V. Lua{\~n}a and J. M. Recio and A. Mart{\'\i}n Pend{\'a}s and M. A. Blanco and L. Pueyo and R. Pandey }, title = { Practical Embedding for Ionic Materials. {I}. {C}rystal adapted pseudopotentials for the {MgO} crystal }, journal = { Phys. Rev. B }, volume = { 64 }, year = { 2001 }, pages = { 104102-1--11 }, abstract = { We present a new method of deriving Effective Core Potentials (ECP) for negative and positive ions. The new ECPs are adapted to ionic crystals and can be used as components of an embedding model in most Quantum Chemistry codes. Cluster-in-the-lattice calculations of several defects and impurity centers in MgO are examined as a test. }, } Regards, V. Lua~na From chemistry-request@server.ccl.net Tue Apr 29 11:40:14 2003 Received: from avogadro.kky.ttu.ee ([193.40.253.225]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TFeER01437 for ; Tue, 29 Apr 2003 11:40:14 -0400 Received: by avogadro.kky.ttu.ee (Postfix, from userid 1000) id B44A82FC7; Tue, 29 Apr 2003 18:40:10 +0300 (EEST) Date: Tue, 29 Apr 2003 18:40:10 +0300 From: Toomas Tamm To: chemistry@ccl.net Subject: visualizing MOs from Turbomole Message-ID: <20030429154010.GA5651@kky.ttu.ee> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i Dear CCLers, Can anyone suggest a tool for visualizing MOs from Turbomole output? The ability to plot a MO energy diagram would be a plus. The software should preferentially be free and for Linux, but other options can be considered. -- Toomas Tamm e-mail: tt-ccl@kky.ttu.ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn Technical University fax: INT+372-620-2796 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From chemistry-request@server.ccl.net Tue Apr 29 13:47:44 2003 Received: from father.chem.ubc.ca ([137.82.7.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3THliR04604 for ; Tue, 29 Apr 2003 13:47:44 -0400 Received: from localhost (sacooke@localhost) by father.chem.ubc.ca (8.12.8/8.12.8) with ESMTP id h3THo7sK019065 for ; Tue, 29 Apr 2003 10:50:07 -0700 Date: Tue, 29 Apr 2003 10:50:07 -0700 (PDT) From: Stephen Cooke To: chemistry@ccl.net Subject: Molden Laplacian Plot options. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Everybody, We have an interest in our laboratory in examining the bonding in rare gas containing molecules through experiment. Accordingly we have begun supplementing our experimental work with theoretical calculations and in particular producing electron density plots of our molecules and also examing the laplacian plots, all using Molden. Of increasing interest is the Laplacian. Molden has 4 plot options for the laplacian, i'm sure many of you will know these are: Euclid, 3D, 3D-X and Space. I can interpret the Euclid and 3D type plots (well just about anyway!) and these appear to be the common way of presenting this type of information. My question is how should one interpret the "Space plot" of the Laplacian? I have examined the online documentation and have not been successful in finding any help. Thank you for your time, Best wishes, Steve Cooke Chemistry Department The University of British Columbia Vancouver Canada sacooke@chem.ubc.ca Tel: (604) 822-2129 Fax: (604) 822-2847 From chemistry-request@server.ccl.net Tue Apr 29 12:03:48 2003 Received: from dirac.bri.nrc.ca ([206.167.189.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TG3mR02310 for ; Tue, 29 Apr 2003 12:03:48 -0400 Received: from localhost (wujih@localhost) by dirac.bri.nrc.ca (8.8.8/8.8.8) with ESMTP id MAA2283164; Tue, 29 Apr 2003 12:01:19 -0400 (EDT) Date: Tue, 29 Apr 2003 12:01:19 -0400 From: Jianhui Wu To: Li Qiang cc: "chemistry@ccl.net" Subject: Re: CCL:SARS design In-Reply-To: <20030429090755.67C6C58FB@smtp03.sohu.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Li Qiang, Check up the following links: (1) http://www.ncbi.nlm.nih.gov/gorf/gorf.html (2)http://www.biochem.ucl.ac.uk/bsm/virus_database/vg (3)http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html Which target in SARS coronavirus would serve as a good drug target? This is a billion dollars question. If you dig into the former work of HIV, you might get some clue. Good luck, Jian Hui Department of Oncology McGill University On Mon, 29 Apr 2002, Li Qiang wrote: > Dear CCLers, > Do you know the SARS, Can you discuss with us about the SARS drug design? > How to get structure from the RNA sequences? > > > Thank you for advance ! > > > > cola > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Apr 29 12:57:46 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3TGvjR03502 for ; Tue, 29 Apr 2003 12:57:45 -0400 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.12.9/8.12.9) with ESMTP id h3TGvidh733598; Tue, 29 Apr 2003 09:57:44 -0700 Date: Tue, 29 Apr 2003 09:57:44 -0700 (PDT) From: Roy Jensen To: chemistry@ccl.net Subject: G03W multiprocessor support? In-Reply-To: <3EB137B9@webmail1> Message-ID: References: <3EB137B9@webmail1> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) All There was hope that the next version of Gaussian, G03W, would support multiple processors. I couldn't find anything on the Gaussian website, nor has Gaussian answered my emails. Does anyone know if it can? Roy Jensen