From owner-chemistry@ccl.net Thu Jul 29 06:15:00 2010 From: "=?ISO-8859-1?Q?Jo=E3o_Henriques?= joao.henriques.32353[*]gmail.com" To: CCL Subject: CCL: Histidine protonation states Message-Id: <-42375-100729061328-18672-uWlhDK/N7XS3Dj6BU+iKgQ[A]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Henriques?= Content-Type: multipart/alternative; boundary=001636c5b55c9ef8e5048c83fa13 Date: Thu, 29 Jul 2010 11:13:00 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [joao.henriques.32353{=}gmail.com] --001636c5b55c9ef8e5048c83fa13 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Iamees, You can either set them by hand depending on the pH you are interested in (protonation states will be fixed during the entire run, which is not realistic), or you can use the open source MEAD (Macroscopic Electrostatics with Atomic Detail) program (see Donald Bashford's papers) in conjugation with your MD run, like it's done in the constant pH MD method I work with. This method is based on the stochastic titration method (see Ant=F3nio Baptista's work, specially this one - doi:10.1063/1.1497164) which allows you to include pH as a constant in the simulations, enabling the pH sensitive sites to titrate in a realistic fashion. Best regards, --=20 Jo=E3o Henriques, Master's Student Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: jmhenriques]=[fc.ul.pt --001636c5b55c9ef8e5048c83fa13 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Iamees,

You can either set them by hand depending o= n the pH you are interested in (protonation states will be fixed during the= entire run, which is not realistic), or you can use the open source MEAD (= Macroscopic Electrostatics with Atomic Detail) program (see Donald Bashford= 's papers) in conjugation with your MD run, like it's done in the c= onstant pH MD method I work with. This method is based on the stochastic ti= tration method (see Ant=F3nio Baptista's work, specially this one - doi= :10.1063/1.1497164) which allows you to include pH as a constant in the sim= ulations, enabling the pH sensitive sites to titrate in a realistic fashion= . =A0

Best regards,

--
Jo=E3o He= nriques, Master's Student
Faculty of Science of the University of Li= sbon
Department of Chemistry and Biochemistry
C8 Building, Room 8.5.4= 7
Campo Grande, 1749-016 Lisbon, Portugal
E-mail: jmhenriques]=[fc.ul.pt
--001636c5b55c9ef8e5048c83fa13-- From owner-chemistry@ccl.net Thu Jul 29 07:20:00 2010 From: "Visvaldas K. coyote_v2002|,|yahoo.com" To: CCL Subject: CCL: Histidine protonation states Message-Id: <-42376-100729071558-4123-Bred89wwmnev8sg/AZCy/A(0)server.ccl.net> X-Original-From: "Visvaldas K." Content-Type: multipart/alternative; boundary="0-223693332-1280402150=:47650" Date: Thu, 29 Jul 2010 04:15:50 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Visvaldas K." [coyote_v2002++yahoo.com] --0-223693332-1280402150=:47650 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Schrodinger's Maestro (free for academics, I believe) allows to prep protei= n for MD run with Histidines at realistic protonation states. Regards, Visvaldas Kairys --- On Thu, 7/29/10, Jo=E3o Henriques joao.henriques.32353[*]gmail.com wrote: > From: Jo=E3o Henriques joao.henriques.32353[*]gmail.com Subject: CCL: Histidine protonation states To: "Kairys, Visvaldas " Date: Thursday, July 29, 2010, 6:13 AM Dear Iamees, You can either set them by hand depending on the pH you are interested in (= protonation states will be fixed during the entire run, which is not realis= tic), or you can use the open source MEAD (Macroscopic Electrostatics with = Atomic Detail) program (see Donald Bashford's papers) in conjugation with y= our MD run, like it's done in the constant pH MD method I work with. This m= ethod is based on the stochastic titration method (see Ant=F3nio Baptista's= work, specially this one - doi:10.1063/1.1497164) which allows you to incl= ude pH as a constant in the simulations, enabling the pH sensitive sites to= titrate in a realistic fashion. =A0=0A Best regards, --=20 Jo=E3o Henriques, Master's Student Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 =0ACampo Grande, 1749-016 Lisbon, Portugal E-mail: jmhenriques*fc.ul.pt =0A=0A=0A=0A=0A --0-223693332-1280402150=:47650 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Schrodinger's Maestro (free for academics, I = believe) allows to prep protein for MD run with Histidines at realistic pro= tonation states.
Regards,
Visvaldas Kairys

--- On Thu, 7/29= /10, Jo=E3o Henriques joao.henriques.32353[*]gmail.com <owner-chemist= ry{:}ccl.net> wrote:

From: Jo=E3o = Henriques joao.henriques.32353[*]gmail.com <owner-chemistry{:}ccl.net><= br>Subject: CCL: Histidine protonation states
To: "Kairys, Visvaldas -id= #zz-" <coyote_v2002{:}yahoo.com>
Date: Thursday, July 29, 2010, 6:13= AM

Dear Iamees,

You can= either set them by hand depending on the pH you are interested in (protona= tion states will be fixed during the entire run, which is not realistic), o= r you can use the open source MEAD (Macroscopic Electrostatics with Atomic Detail) p= rogram (see Donald Bashford's papers) in conjugation with your MD run, like= it's done in the constant pH MD method I work with. This method is based o= n the stochastic titration method (see Ant=F3nio Baptista's work, specially= this one - doi:10.1063/1.1497164) which allows you to include pH as a cons= tant in the simulations, enabling the pH sensitive sites to titrate in a re= alistic fashion.  
=0A

Best regards,

--
Jo=E3o Henriques, Master's Student
Faculty of Sci= ence of the University of Lisbon
Department of Chemistry and Biochemistr= y
C8 Building, Room 8.5.47
=0ACampo Grande, 1749-016 Lisbon, Portugal=
E-mail: jmhenriques*f= c.ul.pt
=0A
=0A

=0A=0A --0-223693332-1280402150=:47650-- From owner-chemistry@ccl.net Thu Jul 29 10:53:00 2010 From: "=?GB2312?B?0vO9oQ==?= janeyin600=-=gmail.com" To: CCL Subject: CCL:G: "Guess=Alter" not executed Message-Id: <-42377-100729104948-398-ImJI+MLUsLk8Ad/+oL+cbA^_^server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=001636e1ea84fba858048c87d79f Date: Thu, 29 Jul 2010 09:49:38 -0500 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600!^!gmail.com] --001636e1ea84fba858048c87d79f Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Hi Jamin, I think you are right. Thank you very much for your response! Jane 2010/7/26 Jamin Krinsky jamink**berkeley.edu > Hi Jane, > If the orbitals you are switching are in the same irreducible > representation in the point group of your molecule (or if you do not have > symmetry), altering the orbital ordering will not change the SCF result, > because the algorithm is trying to give you the ground state. Someone > suggested using "guess=3Donly" and looking at the result. This is a good = idea > because you can verify that the "guess=3Dalter" keyword worked, but when = you > converge that wavefunction it will collapse to your previous result, > assuming your previous result was not a spurious local minimum (in orbita= l > space). Assuming you are using DFT here, note that the theory is only > defined at the ground state for each irreducible rep. > Regards, > Jamin > > > 2010/7/25 =D2=F3=BD=A1 janeyin600|*|gmail.com > > Hi All, >> >> I have a confusion about the "*Guess=3DAlter*" command in Gaussian03. I >> used this command to promote one unpaired electron from sigma orbital to= pi >> orbital, in order to change the molecule form sigma radical to pi radica= l. >> However, the energy, charge and spin density are totally the same as bef= ore. >> Seems like it is not executed at all. >> >> I am pretty sure that I switched the correct orbitals and I kept the >> molecule under Cs symmetry all the time. Does anyone know what caused th= is >> failure? >> >> Thank you very much! >> >> Jane >> > > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink#%#berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > --001636e1ea84fba858048c87d79f Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable
Hi Jamin,
 
I think you are right. Thank you very much for your response!
 
Jane

2010/7/26 Jamin Krinsky jamink**berkeley.edu <owner-chemistry#ccl.net>
Hi Jane,
If the orbitals you = are switching are in the same irreducible representation in the point group= of your molecule (or if you do not have symmetry), altering the orbital or= dering will not change the SCF result, because the algorithm is trying to g= ive you the ground state. Someone suggested using "guess=3Donly" = and looking at the result. This is a good idea because you can verify that = the "guess=3Dalter" keyword worked, but when you converge that wa= vefunction it will collapse to your previous result, assuming your previous= result was not a spurious local minimum (in orbital space). Assuming you a= re using DFT here, note that the theory is only defined at the ground state= for each irreducible rep.
Regards,
Jamin


2010/7/25 =D2=F3=BD=A1 janeyin600|*|gmail.com <= owner-chemistry#%#ccl.net>=20

Hi All,
 
I have a confusion about the "Guess=3DAlter" command = in Gaussian03. I used this command to promote one unpaired electron fr= om sigma orbital to pi orbital, in order to change the molecule form sigma = radical to pi radical. However, the energy, charge and spin density are tot= ally the same as before. Seems like it is not executed at all.
 
I am pretty sure that I switched the correct orbitals and I kept the m= olecule under Cs symmetry all the time. Does anyone know what cau= sed this failure? 
 
Thank you very much!
 
Jane



--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Comp= utation Facility
175 Tan Hall, University of California, Berkeley, CA 94= 720
jamink#%#berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

=

--001636e1ea84fba858048c87d79f-- From owner-chemistry@ccl.net Thu Jul 29 11:27:00 2010 From: "=?GB2312?B?0vO9oQ==?= janeyin600 .. gmail.com" To: CCL Subject: CCL:G: "Guess=Alter" not executed Message-Id: <-42378-100729105119-817-GZX5RivS2mGQPF+lMympyg^^server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=0016364ed6c09983e9048c87dde0 Date: Thu, 29 Jul 2010 09:51:13 -0500 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600[A]gmail.com] --0016364ed6c09983e9048c87dde0 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Thank you Xiaoguang! I am trying "SCF=3DQC" now. It takes a while though. I will let you know what happens. Jane =D4=DA 2010=C4=EA7=D4=C225=C8=D5 =CF=C2=CE=E77:49=A3=AC=D0=BB=D0=A1=B9=E2 x= gxie{:}ynu.edu.cn =D0=B4=B5=C0=A3=BA > Dear Jane, > > Keyword "SCF=3DQC" may be useful for problem. thanks. > > Good luck! > > Xiaoguang Xie > > Yunnan university > > =D4=DA=C4=FA=B5=C4=C0=B4=D0=C5=D6=D0=D4=F8=BE=AD=CC=E1=B5=BD: > >From: "=D2=F3=BD=A1 janeyin600|*|gmail.com" > >Reply-To: "CCL Subscribers" > >To: "Xie, Xiao-Guang " > >Subject: CCL:G: \"Guess=3DAlter\" not executed > >Date:Sun, 25 Jul 2010 18:08:14 -0500 > > > >Hi All, > > > >I have a confusion about the "*Guess=3DAlter*" command in Gaussian03. I = used > >this command to promote one unpaired electron from sigma orbital to pi > >orbital, in order to change the molecule form sigma radical to pi radica= l. > > >However, the energy, charge and spin density are totally the same as bef= ore. > >Seems like it is not executed at all. > > > >I am pretty sure that I switched the correct orbitals and I kept the > >molecule under Cs symmetry all the time. Does anyone know what caused th= is > >failure? > > > >Thank you very much! > > > >Jane > > > > > --0016364ed6c09983e9048c87dde0 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable
Thank you Xiaoguang! I am trying "SCF=3DQC" now. It takes a = while though. I will let you know what happens.
 
Jane 

=D4=DA 2010=C4=EA7=D4=C225=C8=D5 =CF=C2=CE=E77:4= 9=A3=AC=D0=BB=D0=A1=B9=E2 xgxie{:}ynu.edu.cn<= /a> <owner-= chemistry-.-ccl.net>=D0=B4=B5=C0=A3=BA

Dear Jane,

Keyword "SCF=3DQC" may be useful for problem. thanks.

Good luck!

Xiaoguang Xie

Yunnan university

=D4=DA=C4=FA=B5=C4=C0=B4=D0=C5=D6=D0=D4=F8=BE= =AD=CC=E1=B5=BD:
>From: "=D2=F3=BD=A1 janeyin600|*|gmail.com" <<= a href=3D"mailto:owner-chemistry-.-ccl.net" target=3D"_blank">owner-chemistry= -.-ccl.net>
>Reply-To: "CCL Subscribers" <chemistry-.-ccl.net>
>T= o: "Xie, Xiao-Guang " <xgxie-.-ynu.edu.cn>
>Subject: CCL:G: \"Guess=3DAlter\" not exe= cuted
>Date:Sun, 25 Jul 2010 18:08:14 -0500<= br>>
>Hi All,
>
>I have a confusio= n about the "*Guess=3DAlter*" command in=  Gaussian03. I used
>this command to promote one unpaired elec= tron from sigma orbital to pi
>orbital, = ;in order to change the molecule form si= gma radical to pi radical.
>However, the&nbs= p;energy, charge and spin density are totally=  the same as before.
>Seems like it is not executed at all= .
>
>I am pretty sure that I swit= ched the correct orbitals and I kept the=
>molecule under Cs symmetry all the ti= me. Does anyone know what caused this
>= failure?
>
>Thank you very much!
>
>Jane
>=
> 


--0016364ed6c09983e9048c87dde0-- From owner-chemistry@ccl.net Thu Jul 29 13:23:01 2010 From: "Gadzikano Munyuki gadzie(!)gmail.com" To: CCL Subject: CCL:G: Gaussian09 Error Message-Id: <-42379-100729044050-12550-mUq9TnYgG71TYmzznOuwjQ|-|server.ccl.net> X-Original-From: Gadzikano Munyuki Content-Type: multipart/alternative; boundary=0016e64653f05af787048c82b05d Date: Thu, 29 Jul 2010 10:40:39 +0200 MIME-Version: 1.0 Sent to CCL by: Gadzikano Munyuki [gadzie{}gmail.com] --0016e64653f05af787048c82b05d Content-Type: text/plain; charset=ISO-8859-1 Hi all, I am trying to do an optimization job of a calcium-peptide complex using gaussian09. the peptide is quite big, it has 10 residues . I managed to optimize the structure without any problems with a smaller basis set 3-21G. However when i try to adopt a bigger basis set i am getting the error below Any help will be very appreciated.... ----------------------------- -------------- # b3lyp/6-31G Opt=calcfc geom=allcheck guess=read scf=(qc,maxcycle=1000) ------------------------------------------- 1/10=4,29=7,30=1,38=1/1,3; 2/12=2,40=1/2; 3/5=5,11=2,14=-4,16=1,25=1,30=1,71=2,74=-5,116=-2/1,2,3; 4/5=1/1; 5/5=2,38=6,98=1/2; 8/6=4,10=90,11=11/1; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 7/8=1,10=1,25=1/1,2,3,16; 1/10=4,30=1/3; ............................................................ Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. FoFDir/FoFCou used for L=0 through L=1. End of G2Drv Frequency-dependent properties file 721 does not exist. End of G2Drv Frequency-dependent properties file 722 does not exist. IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111111111111111111111 Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. There are 585 degrees of freedom in the 1st order CPHF. IDoFFX=5. 585 vectors produced by pass 0 Test12= 2.74D-13 1.00D-09 XBig12= 1.01D+05 2.93D+02. AX will form 18 AO Fock derivatives at one time. 585 vectors produced by pass 1 Test12= 2.74D-13 1.00D-09 XBig12= 1.16D+04 1.47D+01. 585 vectors produced by pass 2 Test12= 2.74D-13 1.00D-09 XBig12= 4.64D+01 5.44D-01. 582 vectors produced by pass 3 Test12= 2.74D-13 1.00D-09 XBig12= 1.01D-01 1.97D-02. 582 vectors produced by pass 4 Test12= 2.74D-13 1.00D-09 XBig12= 1.18D-04 4.58D-04. 327 vectors produced by pass 5 Test12= 2.74D-13 1.00D-09 XBig12= 9.50D-08 1.64D-05. 16 vectors produced by pass 6 Test12= 2.74D-13 1.00D-09 XBig12= 6.51D-11 3.18D-07. 3 vectors produced by pass 7 Test12= 2.74D-13 1.00D-09 XBig12= 4.67D-14 7.29D-09. Inverted reduced A of dimension 3265 with in-core refinement. NIJ > Max2 in MMCore. Error termination via Lnk1e in /opt/gridware/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010. Job cpu time: 1 days 23 hours 4 minutes 27.7 seconds. File lengths (MBytes): RWF= 31540 Int= 0 D2E= 0 Chk= 96 Scr= 1 failed to open execfile --0016e64653f05af787048c82b05d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,

I am trying to do an optimization job of a calcium-peptide complex using gaussian09. the peptide is quite big, it=A0 has 10 residues=A0 . I managed to optimize the structure without any problems with a smaller basis set 3-21G. However when i try to adopt a bigger basis set i am getting the error below

Any help will be very appreciated....


=A0-------------------= ----------
--------------
=A0# b3lyp/6-31G=A0 Opt=3Dcalcf= c geom=3Dallcheck guess=3Dread scf=3D(qc,maxcycle=3D1000)


=A0---= ----------------------------------------
=A01/10=3D4,29=3D7,30=3D1,38=3D1/1,3;
=A02/12=3D2,40=3D1/2;
=A03/5=3D= 5,11=3D2,14=3D-4,16=3D1,25=3D1,30=3D1,71=3D2,74=3D-5,116=3D-2/1,2,3;
=A0= 4/5=3D1/1;
=A05/5=3D2,38=3D6,98=3D1/2;
=A08/6=3D4,10=3D90,11=3D11/1;<= br>=A011/6=3D1,8=3D1,9=3D11,15=3D111,16=3D1/1,2,10;
=A010/6=3D1/2;
=A06/7=3D2,8=3D2,9=3D2,10=3D2,18=3D1,28=3D1/1;
=A07/8=3D1,10=3D1,25=3D1/= 1,2,3,16;
=A01/10=3D4,30=3D1/3;


.............................= ...............................

=A0Calling FoFCou, ICntrl=3D=A0 3107= FMM=3DT I1Cent=3D=A0=A0 0 AccDes=3D 0.00D+00.
=A0FoFDir/FoFCou used for L=3D0 through L=3D1.
=A0End of G2Drv Frequency= -dependent properties file=A0=A0 721 does not exist.
=A0End of G2Drv Fre= quency-dependent properties file=A0=A0 722 does not exist.
=A0=A0=A0=A0= =A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111111111111111=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111= 111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D1111111111111111111111= 1111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D111111= 11111111111111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Diffe= rentiating once with respect to electric field.
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 with respect to dipole field.=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Differentiating once with respect to nuclea= r coordinates.
=A0=A0=A0=A0=A0=A0=A0=A0=A0 There are=A0=A0 585 degrees o= f freedom in the 1st order CPHF.=A0 IDoFFX=3D5.
=A0=A0=A0 585 vectors pr= oduced by pass=A0 0 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.01D+05 2.93D+02= .
=A0AX will form=A0=A0=A0 18 AO Fock derivatives at one time.
=A0=A0=A0 5= 85 vectors produced by pass=A0 1 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.16= D+04 1.47D+01.
=A0=A0=A0 585 vectors produced by pass=A0 2 Test12=3D 2.7= 4D-13 1.00D-09 XBig12=3D 4.64D+01 5.44D-01.
=A0=A0=A0 582 vectors produced by pass=A0 3 Test12=3D 2.74D-13 1.00D-09 XBi= g12=3D 1.01D-01 1.97D-02.
=A0=A0=A0 582 vectors produced by pass=A0 4 Te= st12=3D 2.74D-13 1.00D-09 XBig12=3D 1.18D-04 4.58D-04.
=A0=A0=A0 327 vec= tors produced by pass=A0 5 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 9.50D-08 1= .64D-05.
=A0=A0=A0=A0 16 vectors produced by pass=A0 6 Test12=3D 2.74D-13 1.00D-09 X= Big12=3D 6.51D-11 3.18D-07.
=A0=A0=A0=A0=A0 3 vectors produced by pass= =A0 7 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 4.67D-14 7.29D-09.
=A0Invert= ed reduced A of dimension=A0 3265 with in-core refinement.
=A0NIJ > Max2 in MMCore.
=A0Error termination via Lnk1e in /opt/gridw= are/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010.
=A0Jo= b cpu time:=A0 1 days 23 hours=A0 4 minutes 27.7 seconds.
=A0File length= s (MBytes):=A0 RWF=3D=A0 31540 Int=3D=A0=A0=A0=A0=A0 0 D2E=3D=A0=A0=A0=A0= =A0 0 Chk=3D=A0=A0=A0=A0 96 Scr=3D=A0=A0=A0=A0=A0 1
failed to open execfile
--0016e64653f05af787048c82b05d-- From owner-chemistry@ccl.net Thu Jul 29 13:58:01 2010 From: "Matt Segall matt.segall%optibrium.com" To: CCL Subject: CCL: Free StarDrop Workshop at ACS Fall Meeting Message-Id: <-42380-100729051914-7020-+WSWHe8948LaxGxHYwkEqg#%#server.ccl.net> X-Original-From: "Matt Segall" Date: Thu, 29 Jul 2010 05:19:13 -0400 Sent to CCL by: "Matt Segall" [matt.segall.:.optibrium.com] We are pleased to announce the StarDrop User Group and Workshop at the ACS March meeting in Boston on August 25th. Join us to see how StarDrop can help to guide decisions on the design and selection of high quality compounds in drug discovery. The program will include a hands-on workshop using StarDrop and presentations by Dr Mikel Moyer, VP Molecular Discovery, Epizyme, and Professor Terry Stouch, Duquesne University and consultant to biotech and pharma. For more information and to register visit www.optibrium.com/news/meetings.php. We hope to see you there! Matt Segall ---- Optibrium Ltd. 7226 IQ Cambridge Beach Drive Cambridge CB25 9TL, UK W: www.optibrium.com E: matt.segall-$-optibrium.com T: +44 1223 815900 F: +44 1223 815907 From owner-chemistry@ccl.net Thu Jul 29 15:20:00 2010 From: "Robert McGibbon rmcgibbo[A]princeton.edu" To: CCL Subject: CCL:G: Gaussian09 Error Message-Id: <-42381-100729150913-15737-vSLTRwP5zvjdbi/xxz1u8A]=[server.ccl.net> X-Original-From: Robert McGibbon Content-Type: multipart/alternative; boundary=0016364178a9cf488f048c8b777e Date: Thu, 29 Jul 2010 15:09:04 -0400 MIME-Version: 1.0 Sent to CCL by: Robert McGibbon [rmcgibbo(0)princeton.edu] --0016364178a9cf488f048c8b777e Content-Type: text/plain; charset=ISO-8859-1 Gadzikano, I'm not entirely sure what your problem is, as I've never seen that error. However, I would not recommend using the 'opt=calcfc' keyword. Computing the force constants at the beginning is very costly and could be where your error is coming. It might be preferable to use the force constants from a freq job with the 3-21G basis set as the initial guess Hessian instead - this can be done with the opt=readfckeyword. Just my $0.02, -robert On Thu, Jul 29, 2010 at 4:40 AM, Gadzikano Munyuki gadzie(!)gmail.com < owner-chemistry+/-ccl.net> wrote: > Hi all, > > I am trying to do an optimization job of a calcium-peptide complex using > gaussian09. the peptide is quite big, it has 10 residues . I managed to > optimize the structure without any problems with a smaller basis set 3-21G. > However when i try to adopt a bigger basis set i am getting the error below > > Any help will be very appreciated.... > > > ----------------------------- > -------------- > # b3lyp/6-31G Opt=calcfc geom=allcheck guess=read scf=(qc,maxcycle=1000) > > > ------------------------------------------- > 1/10=4,29=7,30=1,38=1/1,3; > 2/12=2,40=1/2; > 3/5=5,11=2,14=-4,16=1,25=1,30=1,71=2,74=-5,116=-2/1,2,3; > 4/5=1/1; > 5/5=2,38=6,98=1/2; > 8/6=4,10=90,11=11/1; > 11/6=1,8=1,9=11,15=111,16=1/1,2,10; > 10/6=1/2; > 6/7=2,8=2,9=2,10=2,18=1,28=1/1; > 7/8=1,10=1,25=1/1,2,3,16; > 1/10=4,30=1/3; > > > ............................................................ > > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > FoFDir/FoFCou used for L=0 through L=1. > End of G2Drv Frequency-dependent properties file 721 does not exist. > End of G2Drv Frequency-dependent properties file 722 does not exist. > IDoAtm=11111111111111111111111111111111111111111111111111 > IDoAtm=11111111111111111111111111111111111111111111111111 > IDoAtm=11111111111111111111111111111111111111111111111111 > IDoAtm=11111111111111111111111111111111111111111111 > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > There are 585 degrees of freedom in the 1st order CPHF. > IDoFFX=5. > 585 vectors produced by pass 0 Test12= 2.74D-13 1.00D-09 XBig12= > 1.01D+05 2.93D+02. > AX will form 18 AO Fock derivatives at one time. > 585 vectors produced by pass 1 Test12= 2.74D-13 1.00D-09 XBig12= > 1.16D+04 1.47D+01. > 585 vectors produced by pass 2 Test12= 2.74D-13 1.00D-09 XBig12= > 4.64D+01 5.44D-01. > 582 vectors produced by pass 3 Test12= 2.74D-13 1.00D-09 XBig12= > 1.01D-01 1.97D-02. > 582 vectors produced by pass 4 Test12= 2.74D-13 1.00D-09 XBig12= > 1.18D-04 4.58D-04. > 327 vectors produced by pass 5 Test12= 2.74D-13 1.00D-09 XBig12= > 9.50D-08 1.64D-05. > 16 vectors produced by pass 6 Test12= 2.74D-13 1.00D-09 XBig12= > 6.51D-11 3.18D-07. > 3 vectors produced by pass 7 Test12= 2.74D-13 1.00D-09 XBig12= > 4.67D-14 7.29D-09. > Inverted reduced A of dimension 3265 with in-core refinement. > NIJ > Max2 in MMCore. > Error termination via Lnk1e in > /opt/gridware/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010. > Job cpu time: 1 days 23 hours 4 minutes 27.7 seconds. > File lengths (MBytes): RWF= 31540 Int= 0 D2E= 0 Chk= 96 > Scr= 1 > failed to open execfile > --0016364178a9cf488f048c8b777e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Gadzikano,

I'm not entirely sure what your pro= blem is, as I've never seen that error. However, I would not recommend = using the 'opt=3Dcalcfc' keyword. Computing the force constants at = the beginning is very costly and could be where your error is coming. It mi= ght be preferable to use the force constants from a freq job with the 3-21G= basis set as the initial guess Hessian instead - this can be done with the= opt=3Dreadfc= keyword.

Just my $0.02,
-robert

On Thu, Jul 29, 2010 at 4:40 AM, Gadzikano Munyuki gadzie(= !)gmail.com <owner-chemistry+/-ccl.net> = wrote:
Hi all,

I am trying to do an optimiz= ation job of a calcium-peptide complex using gaussian09. the peptide is quite big, it=A0 has 10 residues=A0 . I managed to optimize the structure without any problems with a smaller basis set 3-21G. However when i try to adopt a bigger basis set i am getting the error below

Any help will be very appreciated....


=A0-------------------= ----------
--------------
=A0# b3lyp/6-31G=A0 Opt=3Dcalcfc geom=3Dal= lcheck guess=3Dread scf=3D(qc,maxcycle=3D1000)


=A0--------------= -----------------------------
=A01/10=3D4,29=3D7,30=3D1,38=3D1/1,3;
=A02/12=3D2,40=3D1/2;
=A03/5=3D= 5,11=3D2,14=3D-4,16=3D1,25=3D1,30=3D1,71=3D2,74=3D-5,116=3D-2/1,2,3;
=A0= 4/5=3D1/1;
=A05/5=3D2,38=3D6,98=3D1/2;
=A08/6=3D4,10=3D90,11=3D11/1;<= br>=A011/6=3D1,8=3D1,9=3D11,15=3D111,16=3D1/1,2,10;
=A010/6=3D1/2;
=A06/7=3D2,8=3D2,9=3D2,10=3D2,18=3D1,28=3D1/1;
=A07/8=3D1,10=3D1,25=3D1/= 1,2,3,16;
=A01/10=3D4,30=3D1/3;


.............................= ...............................

=A0Calling FoFCou, ICntrl=3D=A0 3107= FMM=3DT I1Cent=3D=A0=A0 0 AccDes=3D 0.00D+00.
=A0FoFDir/FoFCou used for L=3D0 through L=3D1.
=A0End of G2Drv Frequency= -dependent properties file=A0=A0 721 does not exist.
=A0End of G2Drv Fre= quency-dependent properties file=A0=A0 722 does not exist.
=A0=A0=A0=A0= =A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111111111111111=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111= 111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D1111111111111111111111= 1111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D111111= 11111111111111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Diffe= rentiating once with respect to electric field.
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 with respect to dipole field.=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Differentiating once with respect to nuclea= r coordinates.
=A0=A0=A0=A0=A0=A0=A0=A0=A0 There are=A0=A0 585 degrees o= f freedom in the 1st order CPHF.=A0 IDoFFX=3D5.
=A0=A0=A0 585 vectors pr= oduced by pass=A0 0 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.01D+05 2.93D+02= .
=A0AX will form=A0=A0=A0 18 AO Fock derivatives at one time.
=A0=A0=A0 5= 85 vectors produced by pass=A0 1 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.16= D+04 1.47D+01.
=A0=A0=A0 585 vectors produced by pass=A0 2 Test12=3D 2.7= 4D-13 1.00D-09 XBig12=3D 4.64D+01 5.44D-01.
=A0=A0=A0 582 vectors produced by pass=A0 3 Test12=3D 2.74D-13 1.00D-09 XBi= g12=3D 1.01D-01 1.97D-02.
=A0=A0=A0 582 vectors produced by pass=A0 4 Te= st12=3D 2.74D-13 1.00D-09 XBig12=3D 1.18D-04 4.58D-04.
=A0=A0=A0 327 vec= tors produced by pass=A0 5 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 9.50D-08 1= .64D-05.
=A0=A0=A0=A0 16 vectors produced by pass=A0 6 Test12=3D 2.74D-13 1.00D-09 X= Big12=3D 6.51D-11 3.18D-07.
=A0=A0=A0=A0=A0 3 vectors produced by pass= =A0 7 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 4.67D-14 7.29D-09.
=A0Invert= ed reduced A of dimension=A0 3265 with in-core refinement.
=A0NIJ > Max2 in MMCore.
=A0Error termination via Lnk1e in /opt/gridw= are/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010.
=A0Jo= b cpu time:=A0 1 days 23 hours=A0 4 minutes 27.7 seconds.
=A0File length= s (MBytes):=A0 RWF=3D=A0 31540 Int=3D=A0=A0=A0=A0=A0 0 D2E=3D=A0=A0=A0=A0= =A0 0 Chk=3D=A0=A0=A0=A0 96 Scr=3D=A0=A0=A0=A0=A0 1
failed to open execfile

--0016364178a9cf488f048c8b777e-- From owner-chemistry@ccl.net Thu Jul 29 17:00:00 2010 From: "Jamin Krinsky jamink-,-berkeley.edu" To: CCL Subject: CCL:G: Gaussian09 Error Message-Id: <-42382-100729165813-16536-A0g1k27MN0izQieGgABO4g]*[server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=000e0cd2de4e13a238048c8cfb9e Date: Thu, 29 Jul 2010 13:57:22 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]|[berkeley.edu] --000e0cd2de4e13a238048c8cfb9e Content-Type: text/plain; charset=ISO-8859-1 Gadzikano, Robert, It is hard for me to tell whether it is a memory or disk space error, but the job is definitely running out of resources during the calculation of force constants. Robert is right that you normally don't need to calculate forces at the beginning of a geometry optimization (the opt=calcfc keyword), however you will need to do a frequency calculation at the end (which will fail similarly with the resources you are allocating). The suggestion of doing the frequencies using a smaller basis is not sound: a vibrational analysis on a structure optimized at a different level of theory is meaningless, because the stationary point will be located at different places in coordinate space for different methods (in this case basis set size). Regards, Jamin On Thu, Jul 29, 2010 at 12:09 PM, Robert McGibbon rmcgibbo[A]princeton.edu < owner-chemistry*ccl.net> wrote: > Gadzikano, > > I'm not entirely sure what your problem is, as I've never seen that error. > However, I would not recommend using the 'opt=calcfc' keyword. Computing the > force constants at the beginning is very costly and could be where your > error is coming. It might be preferable to use the force constants from a > freq job with the 3-21G basis set as the initial guess Hessian instead - > this can be done with the opt=readfckeyword. > > Just my $0.02, > -robert > > > On Thu, Jul 29, 2010 at 4:40 AM, Gadzikano Munyuki gadzie(!)gmail.com < > owner-chemistry.:.ccl.net> wrote: > >> Hi all, >> >> I am trying to do an optimization job of a calcium-peptide complex using >> gaussian09. the peptide is quite big, it has 10 residues . I managed to >> optimize the structure without any problems with a smaller basis set 3-21G. >> However when i try to adopt a bigger basis set i am getting the error below >> >> Any help will be very appreciated.... >> >> >> ----------------------------- >> -------------- >> # b3lyp/6-31G Opt=calcfc geom=allcheck guess=read scf=(qc,maxcycle=1000) >> >> >> ------------------------------------------- >> 1/10=4,29=7,30=1,38=1/1,3; >> 2/12=2,40=1/2; >> 3/5=5,11=2,14=-4,16=1,25=1,30=1,71=2,74=-5,116=-2/1,2,3; >> 4/5=1/1; >> 5/5=2,38=6,98=1/2; >> 8/6=4,10=90,11=11/1; >> 11/6=1,8=1,9=11,15=111,16=1/1,2,10; >> 10/6=1/2; >> 6/7=2,8=2,9=2,10=2,18=1,28=1/1; >> 7/8=1,10=1,25=1/1,2,3,16; >> 1/10=4,30=1/3; >> >> >> ............................................................ >> >> Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. >> FoFDir/FoFCou used for L=0 through L=1. >> End of G2Drv Frequency-dependent properties file 721 does not exist. >> End of G2Drv Frequency-dependent properties file 722 does not exist. >> IDoAtm=11111111111111111111111111111111111111111111111111 >> IDoAtm=11111111111111111111111111111111111111111111111111 >> IDoAtm=11111111111111111111111111111111111111111111111111 >> IDoAtm=11111111111111111111111111111111111111111111 >> Differentiating once with respect to electric field. >> with respect to dipole field. >> Differentiating once with respect to nuclear coordinates. >> There are 585 degrees of freedom in the 1st order CPHF. >> IDoFFX=5. >> 585 vectors produced by pass 0 Test12= 2.74D-13 1.00D-09 XBig12= >> 1.01D+05 2.93D+02. >> AX will form 18 AO Fock derivatives at one time. >> 585 vectors produced by pass 1 Test12= 2.74D-13 1.00D-09 XBig12= >> 1.16D+04 1.47D+01. >> 585 vectors produced by pass 2 Test12= 2.74D-13 1.00D-09 XBig12= >> 4.64D+01 5.44D-01. >> 582 vectors produced by pass 3 Test12= 2.74D-13 1.00D-09 XBig12= >> 1.01D-01 1.97D-02. >> 582 vectors produced by pass 4 Test12= 2.74D-13 1.00D-09 XBig12= >> 1.18D-04 4.58D-04. >> 327 vectors produced by pass 5 Test12= 2.74D-13 1.00D-09 XBig12= >> 9.50D-08 1.64D-05. >> 16 vectors produced by pass 6 Test12= 2.74D-13 1.00D-09 XBig12= >> 6.51D-11 3.18D-07. >> 3 vectors produced by pass 7 Test12= 2.74D-13 1.00D-09 XBig12= >> 4.67D-14 7.29D-09. >> Inverted reduced A of dimension 3265 with in-core refinement. >> NIJ > Max2 in MMCore. >> Error termination via Lnk1e in >> /opt/gridware/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010. >> Job cpu time: 1 days 23 hours 4 minutes 27.7 seconds. >> File lengths (MBytes): RWF= 31540 Int= 0 D2E= 0 Chk= 96 >> Scr= 1 >> failed to open execfile >> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink*berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --000e0cd2de4e13a238048c8cfb9e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Gadzikano, Robert,

It is hard for me to tell whether it is a memory = or disk space error, but the job is definitely running out of resources dur= ing the calculation of force constants. Robert is right that you normally d= on't need to calculate forces at the beginning of a geometry optimizati= on (the opt=3Dcalcfc keyword), however you will need to do a frequency calc= ulation at the end (which will fail similarly with the resources you are al= locating). The suggestion of doing the frequencies using a smaller basis is= not sound: a vibrational analysis on a structure optimized at a different = level of theory is meaningless, because the stationary point will be locate= d at different places in coordinate space for different methods (in this ca= se basis set size).

Regards,
Jamin


On Thu, Jul 29,= 2010 at 12:09 PM, Robert McGibbon rmcgibbo[A]princeton.edu <owner-chemistry*ccl.net> wrote:
Gadzikano,

I'm not entirely sure what your problem is, as I'= ;ve never seen that error. However, I would not recommend using the 'op= t=3Dcalcfc' keyword. Computing the force constants at the beginning is = very costly and could be where your error is coming. It might be preferable= to use the force constants from a freq job with the 3-21G basis set as the= initial guess Hessian instead - this can be done with the opt=3Dreadfc keyword.

Just my $0.02,
-robert


On Thu, Jul 29, 2010 a= t 4:40 AM, Gadzikano Munyuki gadzie(!)gmail.com <owner-chemistry.:.ccl.net> wrote:
Hi all,

I = am trying to do an optimization job of a calcium-peptide complex using gaussian09. the peptide is quite big, it=A0 has 10 residues=A0 . I managed to optimize the structure without any problems with a smaller basis set 3-21G. However when i try to adopt a bigger basis set i am getting the error below

Any help will be very appreciated....


=A0-------------------= ----------
--------------
=A0# b3lyp/6-31G=A0 Opt=3Dcalcfc geom=3Dal= lcheck guess=3Dread scf=3D(qc,maxcycle=3D1000)


=A0--------------= -----------------------------
=A01/10=3D4,29=3D7,30=3D1,38=3D1/1,3;
=A02/12=3D2,40=3D1/2;
=A03/5=3D= 5,11=3D2,14=3D-4,16=3D1,25=3D1,30=3D1,71=3D2,74=3D-5,116=3D-2/1,2,3;
=A0= 4/5=3D1/1;
=A05/5=3D2,38=3D6,98=3D1/2;
=A08/6=3D4,10=3D90,11=3D11/1;<= br>=A011/6=3D1,8=3D1,9=3D11,15=3D111,16=3D1/1,2,10;
=A010/6=3D1/2;
=A06/7=3D2,8=3D2,9=3D2,10=3D2,18=3D1,28=3D1/1;
=A07/8=3D1,10=3D1,25=3D1/= 1,2,3,16;
=A01/10=3D4,30=3D1/3;


.............................= ...............................

=A0Calling FoFCou, ICntrl=3D=A0 3107= FMM=3DT I1Cent=3D=A0=A0 0 AccDes=3D 0.00D+00.
=A0FoFDir/FoFCou used for L=3D0 through L=3D1.
=A0End of G2Drv Frequency= -dependent properties file=A0=A0 721 does not exist.
=A0End of G2Drv Fre= quency-dependent properties file=A0=A0 722 does not exist.
=A0=A0=A0=A0= =A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111111111111111=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D11111111111111111111111111111111111111= 111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D1111111111111111111111= 1111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 IDoAtm=3D111111= 11111111111111111111111111111111111111
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Diffe= rentiating once with respect to electric field.
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 with respect to dipole field.=
=A0=A0=A0=A0=A0=A0=A0=A0=A0 Differentiating once with respect to nuclea= r coordinates.
=A0=A0=A0=A0=A0=A0=A0=A0=A0 There are=A0=A0 585 degrees o= f freedom in the 1st order CPHF.=A0 IDoFFX=3D5.
=A0=A0=A0 585 vectors pr= oduced by pass=A0 0 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.01D+05 2.93D+02= .
=A0AX will form=A0=A0=A0 18 AO Fock derivatives at one time.
=A0=A0=A0 5= 85 vectors produced by pass=A0 1 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 1.16= D+04 1.47D+01.
=A0=A0=A0 585 vectors produced by pass=A0 2 Test12=3D 2.7= 4D-13 1.00D-09 XBig12=3D 4.64D+01 5.44D-01.
=A0=A0=A0 582 vectors produced by pass=A0 3 Test12=3D 2.74D-13 1.00D-09 XBi= g12=3D 1.01D-01 1.97D-02.
=A0=A0=A0 582 vectors produced by pass=A0 4 Te= st12=3D 2.74D-13 1.00D-09 XBig12=3D 1.18D-04 4.58D-04.
=A0=A0=A0 327 vec= tors produced by pass=A0 5 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 9.50D-08 1= .64D-05.
=A0=A0=A0=A0 16 vectors produced by pass=A0 6 Test12=3D 2.74D-13 1.00D-09 X= Big12=3D 6.51D-11 3.18D-07.
=A0=A0=A0=A0=A0 3 vectors produced by pass= =A0 7 Test12=3D 2.74D-13 1.00D-09 XBig12=3D 4.67D-14 7.29D-09.
=A0Invert= ed reduced A of dimension=A0 3265 with in-core refinement.
=A0NIJ > Max2 in MMCore.
=A0Error termination via Lnk1e in /opt/gridw= are/gaussian/g09/linda-exe/l1002.exel at Thu Jul 22 19:33:56 2010.
=A0Jo= b cpu time:=A0 1 days 23 hours=A0 4 minutes 27.7 seconds.
=A0File length= s (MBytes):=A0 RWF=3D=A0 31540 Int=3D=A0=A0=A0=A0=A0 0 D2E=3D=A0=A0=A0=A0= =A0 0 Chk=3D=A0=A0=A0=A0 96 Scr=3D=A0=A0=A0=A0=A0 1
failed to open execfile




--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink*berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--000e0cd2de4e13a238048c8cfb9e-- From owner-chemistry@ccl.net Thu Jul 29 17:34:01 2010 From: "Tatsiana Kirys tatsiana(~)ku.edu" To: CCL Subject: CCL: charmm energy Message-Id: <-42383-100729164004-13111-eNfTnMjv7ml13FVR/qESnA]![server.ccl.net> X-Original-From: "Tatsiana Kirys" Date: Thu, 29 Jul 2010 16:40:03 -0400 Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] Hi all, i calculate protein energy using enrCHARMM.pl script. i run it with gb and without for the same protein file. enerCHARMM.pl -out total -log file.log file.pdb BONDs 92.56954 ANGLes 336.00337 UREY-b 24.08096 DIHEdrals 604.46805 CMAPs -134.62511 VDWaals -476.01682 ELEC -2041.80015 enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb BONDs 92.56954 ANGLes 336.00337 UREY-b 24.08096 DIHEdrals 604.46805 CMAPs -134.62511 VDWaals -485.01639 ELEC -2021.31359 ASP 102.42587 GBEnr -1479.15727 i dont understand why Electrostatic and VdW energy terms are different. Any help will be very appreciated!!! From owner-chemistry@ccl.net Thu Jul 29 18:25:00 2010 From: "Venable, Richard (NIH/NHLBI) E venabler^^^nhlbi.nih.gov" To: CCL Subject: CCL: charmm energy Message-Id: <-42384-100729182353-21846-qnFGuHQYivgPpzzCA9hPVQ]-[server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 29 Jul 2010 18:23:24 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler:+:nhlbi.nih.gov] I suggest posting your question to the MMTSB forum at www.charmm.org -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] Hi all, i calculate protein energy using enrCHARMM.pl script. i run it with gb and without for the same protein file. enerCHARMM.pl -out total -log file.log file.pdb BONDs 92.56954 ANGLes 336.00337 UREY-b 24.08096 DIHEdrals 604.46805 CMAPs -134.62511 VDWaals -476.01682 ELEC -2041.80015 enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb BONDs 92.56954 ANGLes 336.00337 UREY-b 24.08096 DIHEdrals 604.46805 CMAPs -134.62511 VDWaals -485.01639 ELEC -2021.31359 ASP 102.42587 GBEnr -1479.15727 i dont understand why Electrostatic and VdW energy terms are different. Any help will be very appreciated!!!