From chemistry-request@ccl.net Thu Jun 30 00:18:23 2005 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5U4IJaQ021828 for ; Thu, 30 Jun 2005 00:18:19 -0400 Received: from [127.0.0.1] (x2-04b-73.goldrush.com [64.162.11.73]) by smtp.goldrush.com (8.12.8/8.12.8) with ESMTP id j5U4I9Aw006192; Wed, 29 Jun 2005 21:18:20 -0700 Message-ID: <42C3727B.9060203[at]goldrush.com> Date: Wed, 29 Jun 2005 21:18:03 -0700 From: Steve Bowlus User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry[at]ccl.net, eduard[at]stark.udg.es Subject: Re: CCL:advice on semiempirics References: <42C2F456.3040507[at]iqc.udg.es> In-Reply-To: <42C2F456.3040507[at]iqc.udg.es> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-MailScanner: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: chezbowlus[at]goldrush.com X-Spam-Status: No, score=0.1 required=5.0 tests=DNS_FROM_AHBL_RHSBL autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net PM3 would be an option. If you are using a version of MOPAC or AMPAC, pay close attention to the keywords which might speed up convergence. There are many combinations of options in MOPAC which may help. You may also be able to invoke some local symmetry. Cheers, Steve Eduard Matito wrote: > Hi CCLers! > > I pretend to perform a calculation of huge polybenzenoid hidrocarbons > but I > have no experience on semiempirical calculations. At first, I have > tried am1 > but I haven't succeeded converging the structures. Is there any other > semiempirical > method suitable for such systems? > Thanks in advance, > Eduard > From chemistry-request@ccl.net Thu Jun 30 02:26:35 2005 Received: from fungible9.mail.rice.edu (fungible9-dmfe1.mail.rice.edu [128.42.59.179]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5U6QOUL005220 for ; Thu, 30 Jun 2005 02:26:25 -0400 Received: from localhost (unknown [128.42.58.160]) by fungible9.mail.rice.edu (Postfix) with ESMTP id CFE871DB58; Thu, 30 Jun 2005 00:30:53 -0500 (CDT) Received: from fungible9.mail.rice.edu ([128.42.58.179]) by localhost (scan1.mail.rice.edu [128.42.58.160]) (amavisd-new, port 10024) with LMTP id 14459-01-45; Thu, 30 Jun 2005 00:30:53 -0500 (CDT) Received: from webmail3.mail.rice.edu (unknown [128.42.58.153]) by fungible9.mail.rice.edu (Postfix) with ESMTP id 0B4C01DB16; Thu, 30 Jun 2005 00:30:53 -0500 (CDT) Received: (from cwis@localhost) by webmail3.mail.rice.edu (8.12.9/8.12.8) id j5U5URUa009903; Thu, 30 Jun 2005 00:30:27 -0500 (CDT) X-Authentication-Warning: webmail3.mail.rice.edu: cwis set sender to enb (a) rice.edu using -f Received: from cpe-24-160-115-191.houston.res.rr.com (cpe-24-160-115-191.houston.res.rr.com [24.160.115.191]) by webmail.mail.rice.edu (IMP) with HTTP for ; Thu, 30 Jun 2005 00:30:26 -0500 Message-ID: <1120109426.42c38372da935 (a) webmail.mail.rice.edu> Date: Thu, 30 Jun 2005 00:30:26 -0500 From: enb (a) rice.edu To: chemistry (a) ccl.net, Steve Bowlus Cc: chemistry (a) ccl.net, eduard (a) stark.udg.es Subject: Re: CCL:advice on semiempirics References: <42C2F456.3040507 (a) iqc.udg.es> <42C3727B.9060203 (a) goldrush.com> In-Reply-To: <42C3727B.9060203 (a) goldrush.com> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.4 X-Virus-Scanned: by amavis-2.1.2 at scan1.mail.rice.edu X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net I think the central question would be whether your are able to a) obtain an energy of a given geometry and b) obtain a second geometry with a lower energy (and not necessarily in the second cycle, but over the course of a few cycles). If you have those two things, it is not a semiemprics problem, it is an optimization problem. Consider what optimization procedure you are using (you may want to try a steepest descent for a while before switching to another algorithm). Also, geometry optimization criteria were in most cases designed for small molecules, and may be overly tight for large systms. It may also be advantageous to use redundant internal coordinates rather than cartesian coordinates for optimization. Finally, you have to consider whether the molecule has a lot of degrees of freedom (i.e. it is very floppy) and whether the potential energy surface may be very flat, which will make the task even more difficult. I believe the Merz group (Penn State) has recently published some studies with optimization of large biomolecules and semiempirical methods. Ed Brothers. Quoting Steve Bowlus : > PM3 would be an option. If you are using a version of MOPAC or AMPAC, > pay close attention to the keywords which might speed up convergence. > There are many combinations of options in MOPAC which may help. You may > also be able to invoke some local symmetry. > > Cheers, > Steve > > > Eduard Matito wrote: > > > Hi CCLers! > > > > I pretend to perform a calculation of huge polybenzenoid hidrocarbons > > but I > > have no experience on semiempirical calculations. At first, I have > > tried am1 > > but I haven't succeeded converging the structures. Is there any other > > semiempirical > > method suitable for such systems? > > Thanks in advance, > > Eduard > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY (a) ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST (a) ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jun 30 02:06:36 2005 Received: from smtp05.mrf.mail.rcn.net (smtp05.mrf.mail.rcn.net [207.172.4.64]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5U66XOv004073 for ; Thu, 30 Jun 2005 02:06:33 -0400 Received: from 209-6-216-37.c3-0.smr-ubr3.sbo-smr.ma.cable.rcn.com (HELO anick000) (209.6.216.37) by smtp05.mrf.mail.rcn.net with SMTP; 30 Jun 2005 00:39:18 -0400 X-IronPort-AV: i="3.93,243,1115006400"; d="scan'208,217"; a="56344163:sNHT36548756" Message-ID: <001501c57d2d$42de6a80$25d806d1 (a) cable.rcn.com> From: "David J Anick" To: References: <20050622094046.65369.qmail (a) web86901.mail.ukl.yahoo.com> <42BA6CB4.3090707 (a) cosmologic.de> <755a1e3b050629023528b0a3e4 (a) mail.gmail.com> Subject: Re: CCL:Hydrogen-Bond in Gaussian Date: Thu, 30 Jun 2005 00:36:19 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01C57D0B.BB9A6FE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_50_60,HTML_MESSAGE autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C57D0B.BB9A6FE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Pradyumna, This may or may not help. I have been doing this kind of calculation a lot with water clusters, i.e. X =3D Y =3D O, but the principles should be the same for any X, Y. You can expect to find that there will be some systems where the PES has no local minimum of the form X-H -- Y, and others where there is no local minimum of the form X -- H-Y. In these cases you will either want to compute a relaxed PES as a function of the X-H or H-Y distance, or pick a single "reasonable" value for this distance and compute with it fixed. How can you tell if there's a PES local min? Here's what I do. If I don't easily find a local min, or it seems like a "borderline case" where the min, if it exits, is very shallow, then I will fix the X-H distance and do a constrained optimization. Then I will take the constrained geom and use that as the starting point for an unconstrained optimization. The idea is, if there is a PES min, you will have found it or be very close to it, so you should fall into it with the second calc. A shallow min can be missed if the other params are not optimized first, since the fastest downhill path might scoot right around the min you are after. You many have to give some thought, based on other examples you have run using whatever your model is, as to what is the best initial H - X distance to use as the constraint. For water clusters I set O - H to be between 1.06 to 1.08 A, which is what I have found it to be in cases where the PES minimum is very shallow. If you follow this two-step process and, on the second step, the proton proceeds to transfer to Y during optimization, then you almost certainly have a PES without a local min for H-X -- Y. I hope this is helpful. David Anick PhD MD (Harvard Medical School) ----- Original Message -----=20 From: Pradyumna Shaakuntal Singh=20 To: chemistry (a) ccl.net=20 Sent: Wednesday, June 29, 2005 5:35 AM Subject: CCL:Hydrogen-Bond in Gaussian Hello, I'm trying to study the energetics of proton transfer in = hydrogen-bonded systems using ab initio methods.=20 For any H-bond pair X-H -----Y-Z (where the proton on X-H is = hydrogen-bonded to Y on Y-Z), when I do an optimization of the = structure, is there a way in Gaussian, by which I can ensure that the = proton stays explicitly bonded to X, so that it doesnt travel too far = afield and bond to Y. Further, if I do want the proton to bond to Y but remain H-bonded to = X- (-X ------ H-Y-Z), how can I optimize this configuration. Essentially, I wish to have some control over where the proton is = (without really freezing the proton coordinate entirely), and then = perform the optimizations. Any suggestions are appreciated. Thanks, Pradyumna ------=_NextPart_000_0012_01C57D0B.BB9A6FE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Pradyumna,
 
This may or may not help.
 
I have been doing this kind of = calculation a lot=20 with water clusters,
i.e. X =3D Y =3D O, but the principles = should be the=20 same for any X, Y.
 
You can expect to find that there will = be some=20 systems where
the PES has no local minimum of the = form X-H -- Y,=20 and others
where there is no local minimum of the = form X --=20 H-Y.  In these
cases you will either want to compute a = relaxed PES=20 as a function
of the X-H or H-Y distance, or pick a = single=20 "reasonable" value for
this distance and compute with it=20 fixed.
 
How can you tell if there's a PES local = min? =20 Here's what I do.
If I don't easily find a local min, or = it seems=20 like a "borderline case"
where the min, if it exits, is very = shallow, then I=20 will fix the X-H
distance and do a constrained = optimization. =20 Then I will take the
constrained geom and use that as the = starting point=20 for an
unconstrained optimization.  The = idea is, if=20 there is a PES min,
you will have found it or be very close = to it, so=20 you should fall
into it with the second calc.  A = shallow min=20 can be missed if
the other params are not optimized = first, since the=20 fastest
downhill path might scoot right around = the min you=20 are after.
 
You many have to give some thought, = based on other=20 examples
you have run using whatever your model = is, as to=20 what is the
best initial H - X distance to use as = the=20 constraint.  For water
clusters I set O - H to be between 1.06 = to 1.08 A,=20 which is what
I have found it to be in cases = where the=20 PES minimum is very = shallow.
 
If you follow this two-step process = and, on the=20 second step,
the proton proceeds to transfer to Y = during=20 optimization, then
you almost certainly have a PES without = a local min=20 for H-X -- Y.
 
I hope this is helpful.
 
David Anick PhD MD
(Harvard Medical School)
 
----- Original Message -----
From:=20 Pradyumna Shaakuntal = Singh
Sent: Wednesday, June 29, 2005 = 5:35=20 AM
Subject: CCL:Hydrogen-Bond in=20 Gaussian

Hello,

I'm trying to study the energetics of = proton=20 transfer in hydrogen-bonded systems using ab initio methods.
For = any=20 H-bond pair X-H -----Y-Z  (where the proton on X-H is = hydrogen-bonded to=20 Y on Y-Z), when I do an optimization of the structure, is there a way = in=20 Gaussian, by which I can ensure that the proton stays explicitly = bonded to X,=20 so that it doesnt travel too far afield and bond to Y.

Further, = if I do=20 want the proton to bond to Y but remain H-bonded to X-  (-X = ------=20 H-Y-Z), how can I optimize this configuration.

Essentially, I = wish to=20 have some control over where the proton is (without really freezing = the proton=20 coordinate entirely), and then perform the optimizations. Any = suggestions are=20 = appreciated.

Thanks,
Pradyumna
------=_NextPart_000_0012_01C57D0B.BB9A6FE0-- From chemistry-request@ccl.net Thu Jun 30 08:22:19 2005 Received: from nenu.edu.cn ([202.198.129.55]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5UCMAe3018868 for ; Thu, 30 Jun 2005 08:22:11 -0400 Received: (eyou send program); Thu, 30 Jun 2005 19:45:14 +0800 Message-ID: <320131914.03018 () nenu.edu.cn> Received: from 202.198.136.127 by mail.nenu.edu.cn with HTTP; Thu, 30 Jun 2005 19:45:14 +0800 X-WebMAIL-MUA: [202.198.136.127] From: "QnUqDH" To: chemistry () ccl.net Date: Thu, 30 Jun 2005 19:45:14 +0800 Reply-To: "QnUqDH" Subject: transition state Content-Type: text/plain X-Spam-Status: No, score=4.2 required=5.0 tests=DEAR_SOMETHING, DNS_FROM_RFC_ABUSE,DNS_FROM_RFC_WHOIS,FROM_ENDS_IN_NUMS, HEAD_ILLEGAL_CHARS,MSGID_FROM_MTA_HEADER autolearn=no version=3.0.4 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear sir: I have two questions to ask you. first,how can we get enthalpy and Gibbs free energy from the output file of frequence calculation. sencond, how to caculate Hessian in finding transition state in Gaussian 98. From chemistry-request@ccl.net Wed Jun 29 22:07:25 2005 Received: from mx1.ustc.edu.cn (ns.ustc.edu.cn [202.38.64.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5U27Jsx021889; Wed, 29 Jun 2005 22:07:20 -0400 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.11.6/8.11.6) with SMTP id j5U23Yf23938; Thu, 30 Jun 2005 10:03:34 +0800 Message-Id: <200506300203.j5U23Yf23938 >< mx1.ustc.edu.cn> Date: Thu, 30 Jun 2005 10:05:25 +0800 From: "Ding Xunlei" < ustc.edu.cn> Reply-To: dxl >< ustc.edu.cn To: "chemistry" < ccl.net>, "chemistry-request" < ccl.net>, "help" < gaussian.com> Subject: Gaussian freq calculation error Organization: University of Science and Technology of China X-mailer: Foxmail 5.0 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Spam-Status: No, score=2.6 required=5.0 tests=DEAR_SOMETHING, DNS_FROM_RFC_ABUSE,DNS_FROM_RFC_WHOIS,MIME_BASE64_BLANKS, MIME_BASE64_TEXT autolearn=no version=3.0.4 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id j5U27Psx021914 Dear Sir/Madam#: I did a Gaussian calculation and error occured as below. I know that this error may happen when read a non-exist chk file, or rwf is out of range. But in my work, the head of the input file is: ------------------- %mem=800mb %nproc=6 %rwf=a,1gb,b,1gb,c,1gb,d,1gb,e,1gb,f,1gb,g,1gb # cis(root=1,nstate=1,direct)/6-311+g(d,p) freq Punch=Derivatives ------------------- And in the output files, only a.rwf and b.rwf were written. Then what's wrong with my calculation? !!!! AX will form 96 AO Fock derivatives at one time. 96 vectors were produced by pass 1. 96 vectors were produced by pass 2. 96 vectors were produced by pass 3. 96 vectors were produced by pass 4. 96 vectors were produced by pass 5. 96 vectors were produced by pass 6. 62 vectors were produced by pass 7. 3 vectors were produced by pass 8. 3 vectors were produced by pass 9. Inv2: IOpt= 1 Iter= 1 AM= 5.89D-15 Conv= 1.00D-12. Inverted reduced A of dimension 740 with in-core refinement. End of Minotr Frequency-dependent properties file 721 does not exist. Doing CIS second derivatives. This link is doing 99 degrees of freedom Form MO integral derivatives with frozen-active canonical formalism. CisSec: MDV= 104857342 Frozen orbitals handled with amplitudes over full window. CISAX will form 50 AO SS matrices at one time. Operation on file out of range. FileIO: IOper= 1 IFilNo(1)=-19990 Len= 0 IPos= 1318400 Q=***************** dumping /fiocom/, unit = 1 NFiles = 120 SizExt = 524288 WInBlk = 1024 defal = T LstWrd = 255081472 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 0 Base 145439136 14106081 3687424 5516288 1356800 3748864 5299270 16762470 End 145439744 14106624 3689472 5533696 1357824 3773440 5300224 17079296 End1 145439744 14106624 3689472 5533696 1357824 3773440 5300224 17079296 Wr Pntr 145439136 14106081 3687424 5474304 1356800 3695616 5299270 16762470 Rd Pntr 145439136 14106081 3687424 5474304 1356800 3695616 5299270 16762470 Length 608 543 2048 17408 1024 24576 954 316826 .................... dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 1024 defal = T LstWrd = 66560 FType=2 FMxFil=10000 Number 0 Base 40960 End 66560 End1 66560 Wr Pntr 40960 Rd Pntr 40960 Length 25600 Error termination in NtrErr: NtrErr Called from FileIO. Thank you for your help! Yours sincerely, Ding Xunlei 2005-06-30 ______________________________________________ From chemistry-request@ccl.net Thu Jun 30 12:56:42 2005 Received: from trentu.ca (mxbob.trentu.ca [192.75.12.131]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5UGub66008827 for ; Thu, 30 Jun 2005 12:56:37 -0400 Received: (qmail 3074 invoked by uid 510); 30 Jun 2005 16:56:31 -0000 Received: from 209.42.102.117 by mxbob (envelope-from , uid 502) with qmail-scanner-1.24 (fsecure: 4.52/2461/libra database 2005-06-21/orion database 2005-06-29/avp(2005-06-29). spamassassin: 3.0.2. Clear:RC:1(209.42.102.117):. Processed in 0.084947 secs); 30 Jun 2005 16:56:31 -0000 X-Qmail-Scanner-Mail-From: elewars*&*trentu.ca via mxbob X-Qmail-Scanner: 1.24 (Clear:RC:1(209.42.102.117):. Processed in 0.084947 secs) Received: from unknown (HELO trentu.ca) (209.42.102.117) by trentu.ca with SMTP; 30 Jun 2005 16:56:31 -0000 Message-ID: <42C423C6.40003*&*trentu.ca> Date: Thu, 30 Jun 2005 12:54:30 -0400 From: errol lewars User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry*&*ccl.net Subject: Re: CCL:transition state References: <320131914.03018*&*nenu.edu.cn> In-Reply-To: <320131914.03018*&*nenu.edu.cn> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=1.2 required=5.0 tests=DEAR_SOMETHING, DNS_FROM_RFC_ABUSE,FORGED_RCVD_HELO autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net 2005 June 30 Hello, Gaussian gives enthalpy and Gibbs free energy when you do a frequency calculation (which to be valid must be done using exactly the same level as was used for the geometry optimization, for example HF/3-21G for both). The values are printed right after the frequencies, e.g. Zero-point correction= 0.173654 (Hartree/Particle) Thermal correction to Energy= 0.199937 Thermal correction to Enthalpy= 0.200882 Thermal correction to Gibbs Free Energy= 0.117979 Sum of electronic and zero-point Energies= -2156.346839 Sum of electronic and thermal Energies= -2156.320555 Sum of electronic and thermal Enthalpies= -2156.319611 Sum of electronic and thermal Free Energies= -2156.402514 The values of interest to you are probably (1) Sum of electronic and zero-point Energies, (2) Sum of electronic and thermal Enthalpies, (3) Sum of electronic and thermal Free Energies (1) is the sum of the "raw" energy (electronic energy + internuclear repulsion, best located at the end of an optimization just before "RSMD", e.g.: HF =-2156.520493|RMSD=1.429e-009...) and by subtraction from other (1)-type values gives 0 K enthalpy differences (since at 0 K S = 0). (2) is the enthalpy at 298.15 K and 1.0000 atmosphere ("room temperature and pressure") . Subtraction from other (2)-type values gives enthalpy differences at room temperature/pressure. (3) is analogous to (2); substitute "Gibbs free energy" for "enthalpy". Look at the relevant Gaussian White Paper on their website. As for the Hessian of a transition state, I suppose you want to see if this has one negative eigenvalue; so just ask Gaussian to calculate the frequencies (I assume you have the optimized TS; that's another problem) and see if there is exactly one imaginary vibrational freq. EL ===== QnUqDH wrote: >Dear sir: > I have two questions to ask you. first,how can we get enthalpy and Gibbs >free energy from the output file of frequence calculation. sencond, how to >caculate Hessian in finding transition state in Gaussian 98. > > > = This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY*&*ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*&*ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > From chemistry-request@ccl.net Thu Jun 30 11:28:20 2005 Received: from pohl.acpub.duke.edu (pohl.acpub.duke.edu [152.3.233.64]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5UFSHWQ001718 for ; Thu, 30 Jun 2005 11:28:17 -0400 Received: from godzilla.acpub.duke.edu (godzilla.acpub.duke.edu [152.3.233.25]) by pohl.acpub.duke.edu (8.12.11/8.12.10/Duke-5.0.0) with ESMTP id j5UFSExF026857 for ; Thu, 30 Jun 2005 11:28:15 -0400 Received: (from jz7@localhost) by godzilla.acpub.duke.edu (8.12.10/8.12.9/Submit) id j5UFSBpv009606; Thu, 30 Jun 2005 11:28:11 -0400 (EDT) Date: Thu, 30 Jun 2005 11:28:11 -0400 (EDT) From: jz7 [] duke.edu Sender: jz7 [] duke.edu To: chemistry [] ccl.net Subject: coordination compounds in MM3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.0.3.2, Antispam-Data: 2005.6.30.15 X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Sorry to post my question again. But I didn't get any reply. If anyone has such experience on MM3 (the program Dr. Allinger developed), please share yours with me. I really appreciate your help! --------------------------- I want carry out some calculation on a metal-porphyrin coordination compound using MM3 force field. From MM3 manual, there should be two modification (1,3-electron pair repulsion and bending parameter adjustment). However, I didn't find what special commands I should use to indicate those coordinate bonds (eg. in conjugated systems we have to specify those pi atoms). Would anyone who is familiar with MM3 tell me what kind of special treatment I should apply to the coordination compound? Thanks a lot for the help! ---------------------------- From chemistry-request@ccl.net Thu Jun 30 11:20:44 2005 Received: from pne-smtpout1-sn2.hy.skanova.net (pne-smtpout1-sn2.hy.skanova.net [81.228.8.83]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5UFKdjV001199 for ; Thu, 30 Jun 2005 11:20:40 -0400 Received: from [192.168.0.102] (81.229.201.87) by pne-smtpout1-sn2.hy.skanova.net (7.2.060.1) id 42BFBBD2000BB12F for chemistry [] ccl.net; Thu, 30 Jun 2005 16:38:38 +0200 Mime-Version: 1.0 X-Sender: u42123287 [] m1.421.telia.com (Unverified) Message-Id: In-Reply-To: References: Date: Thu, 30 Jun 2005 16:35:51 +0200 To: chemistry [] ccl.net From: Per-Ola Norrby Subject: Re: CCL:coordination compounds in MM3 Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear Jeny, >I want carry out some calculation on a metal-porphyrin coordination >compound using MM3 force field. From MM3 manual, there should be two >modification (1,3-electron pair repulsion and bending parameter >adjustment). However, I didn't find what special commands I should use to >indicate those coordinate bonds (eg. in conjugated systems we have to >specify those pi atoms). Would anyone who is familiar with MM3 tell me >what kind of special treatment I should apply to the coordination >compound? It depends on which implementation of MM3 you're using, they all differ. If it's the original MM3 program from Allinger, then the atom type determines if it is a coordination center. If it is, any bond to it counts as a coordination bond. In addition to the bending parameters, for optimal results you should also specifically parameterize the bond lengths, but if you're using MM3(96) (or later), I believe you'll get rough guesses > from the parameter estimator, that will serve for quick-and-dirty calculations. You didn't write your name, but I think I recognize the email address, haven't we been in contact before? Best regards, Per-Ola Norrby -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon [] kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@ccl.net Thu Jun 30 11:29:37 2005 Received: from ipex1.johnshopkins.edu (ipex1.johnshopkins.edu [162.129.8.141]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5UFTWXn001831 for ; Thu, 30 Jun 2005 11:29:32 -0400 Received: from jhem1.jhmi.edu (HELO jhumail.jhu.edu) (162.129.8.22) by ipex1.johnshopkins.edu with ESMTP; 30 Jun 2005 11:29:31 -0400 X-BrightmailFiltered: true X-Brightmail-Tracker: AAAAAA== X-IronPort-AV: i="3.93,246,1115006400"; d="scan'208"; a="73535729:sNHT20693192" Received: from [128.220.21.114] by jhumail.jhu.edu (mshttpd); Thu, 30 Jun 2005 11:29:30 -0400 From: SANDEEP KUMAR To: chemistry ## ccl.net Reply-To: kumarsan ## jhu.edu Message-ID: Date: Thu, 30 Jun 2005 11:29:30 -0400 X-Mailer: Sun Java(tm) System Messenger Express 6.1 HotFix 0.11 (built Jan 28 2005) MIME-Version: 1.0 Content-Language: en Subject: Help with MOE X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.6 required=5.0 tests=FORGED_RCVD_HELO, FROM_ENDS_IN_NUMS autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hello: I was wondering if there is a simple way to set the pH for a protein-ligand complex in MOE (Molecular Operations Environment from CCG) for the purpose of molecular electrostatics and simulations calculations. Any input shall be greatly appreciated. Yours sincerely, Sandeep Kumar ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan ## jhu.edu. URL: http://myprofile.cos.com/Kumarsan. or https://jshare.johnshopkins.edu/skumar23/public_html/