From chemistry-request@server.ccl.net Fri Nov 3 07:46:45 2000 Received: from andes.dpi.udec.cl (andes.dpi.udec.CL [152.74.16.14]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA11517 for ; Fri, 3 Nov 2000 07:46:40 -0500 Received: from udec.cl ([152.74.10.171]) by andes.dpi.udec.cl (8.11.0/8.11.0) with ESMTP id eA3D09x12187 for ; Fri, 3 Nov 2000 10:00:09 -0300 (CDT) Message-ID: <3A02B474.82C98ED6@udec.cl> Date: Fri, 03 Nov 2000 09:49:56 -0300 From: "Dr. Antonio Buljan" X-Mailer: Mozilla 4.7C-CCK-MCD {C-UDP; EBM-APPLE} (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: Dipole Moment Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear CCLers, What is the best methodology to calculate dipole moments in diatomic molecules? (for example: CO, LiH, etc.) Dr. Antonio Buljan Departamento de Fisico Quimica Universidad de Concepcion Casilla 160-C CHILE From chemistry-request@server.ccl.net Fri Nov 3 10:58:53 2000 Received: from www2.pobox.sk (www2.pobox.sk [212.5.216.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA12306 for ; Fri, 3 Nov 2000 10:58:52 -0500 Received: from www2.pobox.sk (www2.pobox.sk [212.5.216.12]) by www2.pobox.sk (8.9.3/8.9.3) with SMTP id QAA31641 for ; Fri, 3 Nov 2000 16:58:46 +0100 Date: Fri, 3 Nov 2000 16:58:46 +0100 Message-Id: <200011031558.QAA31641@www2.pobox.sk> From: Shotgun Reply-To: Shotgun Subject: Problems with IRC calculations - update To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=iso-8859-2 X-Pobox-Id: 672187806 X-User-Agent: Mozilla/4.0 (compatible; MSIE 5.5; Windows 98) X-Mailer: POBOX (mico's engine 5.0/3.0.1) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id KAA12307 Hi, I have a problem with some TS's and mostly IRC calculations.I have found transition state with only one imaginary frequency,visualisation shows it could by the correct TS, but IRC calculations lead in both directions to the same final structures with the same value of energy.Please help me with some advice or tricks ,that will solve this problem.Thank you. Thank you for your interest and please forgive my short description of the problem. I am trying to calculate the reaction path of addition of ammines to NCS groups, specially addition of dimers.My current calculations are carried out within Mopac and Gamess on Am1 level.I have located a quite reasonable TS of "jumping " of H from NH3 group - bounded to Carbon atom of NCS group - to another NH3 molecule ( NH4 group is forming ).This Ts has only one imaginary frequency ( value about - 1268 ), but IRC calculations in both directions lead to the same structures with same value of energy - result of irc is that H from NH4 group is being transferred to terminal S of NCS group. Then I have located Ts of transferring H from NH4 group to S ( again only one imaginary frequency ) and again both Irc calculations resulted to the same structures - forming of S-H bond. I hope this more detailed description will help with the solution of this problem. Thank You Stanley,student PF UPJS, Kosice, Slovakia From chemistry-request@server.ccl.net Wed Nov 1 16:30:55 2000 Received: from mailserv.wright.edu (mailserv.wright.edu [130.108.128.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA00815 for ; Wed, 1 Nov 2000 16:30:50 -0500 Received: from CONVERSION-DAEMON by mailserv.wright.edu (PMDF V5.2-33 #39224) id <0G3D00I017R4IS@mailserv.wright.edu> for CHEMISTRY@ccl.net; Wed, 1 Nov 2000 16:30:40 -0500 (EST) Received: from unconfigured (o137142.wright.edu [130.108.137.142]) by mailserv.wright.edu (PMDF V5.2-33 #39224) with SMTP id <0G3D00H8I7R4DA@mailserv.wright.edu> for CHEMISTRY@ccl.net; Wed, 01 Nov 2000 16:30:40 -0500 (EST) Date: Wed, 01 Nov 2000 16:29:49 -0500 From: Kevin Gross Subject: Atoms in Molecules code -- Recap To: CCL Message-id: <003b01c0444a$dd30b780$8e896c82@wright.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Mailer: Microsoft Outlook Express 5.50.4133.2400 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-priority: Normal References: Below is my original posting, followed by the responses. Thanks to all who responded. I especially appreciate Jeff Saxe's help, as he sent me his "cleaned up" AIMPAC code, which I got working on the i386 linux platform with minimal effort. Kevin Gross gross.4@wright.edu Department of Chemistry Wright State University Dayton, Ohio 45435 ----------------------------------- Hi all, I've just started learning about Bader's Atoms in Molecules analysis of wavefunctions and it looks quite interesting. I would like to use his freely available code, AIMPAC, but I am at a loss in getting it to run. I have access to an intel linux box. The AIMPAC code I downloaded from his site did not come with a Makefile or even directions regarding the compilation of the source code. Being a novice at compiling programs, I would sure appreciate guidance from someone who has gotten this code working. I did try searching the CCL archives, but couldn't find anything relevant to compiling AIMPAC. I also came across some stuff regarding PROAIM. Is this a different and/or better implementation of the Atoms in Molecules analysis? If so, where would I find this? I will summarize my results. ----------------------------------- RESPONSES ----------------------------------- I have the AIMPAC code which I cleaned up a couple years ago, and I also added code to allow you to create postscript output. I have sent this to about 10 different people around the world who requested it. I have Makefiles for everything. However I have only run on an SGI, I do not know if you will have problems running on a linux system. You would also likely have to change the 2 lines in the Makefile files which contain the f77 command. If you wish I can email all this to you. Jeff -- Jeffrey D. Saxe BioNumerik Pharmaceuticals, Inc. Suite 1250, 8122 Datapoint Dr., San Antonio, TX 78229 email jeff@bnpi.com phone 210-614-1701 x225 fax 210-615-8030 ----------------------------------- Kevin- Did you try www.chemistry.mcmaster.ca/aimpac? Richard ----------------------------------- I just compliled them with the fortran complier on my SGI O2. I do not know what fortran you will be using on your Linux box, but the command on my O2 is something like this: f77 -o extreme extreme.for This will produce an executable program, named extreme, from the fortran code in extreme.for. I do recall having to re-name the source code files >from Bader's site. You might be using g77 under linux, rather than f77. You might also want to investigate AIM2000. It is a full gui implementation of AIM that runs on pc's under windows. The link for getting this is also on Bader's web site. Good Luck, Steve ----------------------------------- From chemistry-request@server.ccl.net Thu Nov 2 10:06:12 2000 Received: from mailer.psc.edu (mailer.psc.edu [128.182.58.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA05546 for ; Thu, 2 Nov 2000 10:06:11 -0500 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.66.177]) by mailer.psc.edu (8.9.3/8.9.3/psc) with ESMTP id KAA23456 for ; Thu, 2 Nov 2000 10:06:00 -0500 (EST) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.9.3/8.9.3/psc) with ESMTP id KAA11648 for ; Thu, 2 Nov 2000 10:06:00 -0500 (EST) Date: Thu, 2 Nov 2000 10:05:59 -0500 (EST) From: Troy Wymore To: chemistry@server.ccl.net Subject: QM/MM on multiple reaction steps Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCLers, I am setting up some QM/MM calculations on an enzyme which has multiple steps as part of the overall catalytic mechanism. I was thinking that my QM region may be slightly different from one reaction to the next. In this fashion, I can keep my QM region computationally feasible. Any thoughts on whether this would cause any problems in interpretation of results? --Troy Wymore From chemistry-request@server.ccl.net Thu Nov 2 11:37:51 2000 Received: from phnxpop5.phnx.uswest.net (phnxpop5.phnx.uswest.net [206.80.192.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA05897 for ; Thu, 2 Nov 2000 11:37:51 -0500 Received: (qmail 7313 invoked by alias); 2 Nov 2000 16:37:02 -0000 Delivered-To: fixup-CHEMISTRY@ccl.net@fixme Received: (qmail 6548 invoked by uid 0); 2 Nov 2000 16:36:47 -0000 Received: from unknown (HELO bmoritz.asu.edu) (63.228.142.127) by phnxpop5.phnx.uswest.net with SMTP; 2 Nov 2000 16:36:47 -0000 Message-Id: <5.0.0.25.0.20001102092623.009fc290@imap4.asu.edu> X-Sender: bmoritz@imap4.asu.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Thu, 02 Nov 2000 09:37:35 -0700 To: CHEMISTRY@ccl.net From: "Benjamin J. Moritz" Subject: Transition Metals in Gaussian Summary Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====================_50618330==_" --=====================_50618330==_ Content-Type: multipart/alternative; boundary="=====================_50618335==_.ALT" --=====================_50618335==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed I thank all who helped me in overcoming my problem with Gaussian 98 and transition metals basis sets. I was able to overcome the problem with the GEN keyword and the LANL2DZ and am trying other basis as well. Below is a summary of the responses I received. **************************************************************************** If you are performing some calculations on heavy atoms you have to use some pseudo-potential. You cannot simply use a basis set such as e.g. 6-311G**. You can use the following statements (for example): #B3LYP/GEN Opt Pseudo(SDD) or #B3LYP/GEN Opt Pseudo(Read) In the first case G98 will use the Stuttgart pseudo-potential. The GEN keyword specifies that you have to put, at the end of your input file, the basis set for all atoms. I suggest you to have a look to the web site: http://www.emsl.pnl.gov:2080/forms/basisform.html In the second case you have to specify both the basis set (GEN) and the pseudo-potentials. I guess you can also have such a line command: #B3LYP/6-31G Opt Pseudo(SDD) In this case, the 6-31G will be used for light atoms. But you still have to put the pseudo-potentials for heavy ones. You can retrieve the well-formatted basis sets and pseudo potentials in the web site I have just mentioned. *************************************************************** For Hg (and most transition metals) you will need to use a basis set modified with an electrostatic core potential (ECP) which basically removes the core electrons from the atom and replaces them with an empirical potential. G98 comes with the LANL2DZ basis and ECP built-in. If you want to use this basis then set your input like the following: #P RHF/GEN Pseudo=read comments... charge multiplicity molecular specifications C N 0 6-31+G(d') **** Hg 0 LANL2DZ **** Hg 0 LANL2DZ The important parts are the Gen and Pseudo=read - this tells gaussian to look at the end of the input file for the basis set (which can be different for each atom) and the ECP. In the example above I used carbon and nitrogen, you would put the element symbol for whatever atoms are in your molecule there. Let me know if this works for you! ATTACHMENT AT END OF FILE! ****************************************************************** LanL2DZ basis set should be enough as it goes up to atomic number 83 I have used it for a number of transition metals already and had no problems. ****************************************************************** According to the Basis Set Order Form, mercury is only available with the following basis sets: WTBS SBKJC VDZ ECP CRENBL ECP CRENBS ECP Stuttgart RLC ECP Stuttgart RSC ECP Ahlrichs Coulomb Fitting http://www.emsl.pnl.gov:2080/forms/basisform.html They can be used in Gaussian with the GEN keyword. I do not have any experience with any of these basis sets. ************************************************************** You've discovered one of the annoying things about calculations involving elements past chlorine: not all basis sets have been "parameterized" for all elements. Somewhere near the front of the G98 manual is a table of which built-in basis sets are defined for which elements. For your calculations on Hg compounds, your choices are to use one of the built-in basis sets that is defined for that element, or to use gen and pseudo=cards to read in a basis set and pseudopotential that is not built into Gaussian. **************************************************************** Benjamin J. Moritz home (602) 453-9411 Dept. of Chemistry & Biochemistry work (480) 965-8509 Arizona State University Mailto:bmoritz@asu.edu P. O. Box 871604 Tempe, AZ 85287-1604 **************************************************************** "Karma is justice without the satisfaction." --=====================_50618335==_.ALT Content-Type: text/html; charset="us-ascii" I thank all who helped me in overcoming my problem with Gaussian 98 and transition metals basis sets.  I was able to overcome the problem with the GEN keyword and the LANL2DZ and am trying other basis as well. Below is a summary of the responses I received.

****************************************************************************
If you are performing some calculations on heavy atoms you have to use
some pseudo-potential. You cannot simply use a basis set such as e.g.
6-311G**.
You can use the following statements (for example):
#B3LYP/GEN Opt Pseudo(SDD)
or
#B3LYP/GEN Opt Pseudo(Read)
In the first case G98 will use the Stuttgart pseudo-potential. The GEN
keyword specifies that you have to put, at the end of your input file, the
basis set for all atoms. I suggest you to have a look to the web site:
http://www.emsl.pnl.gov:2080/forms/basisform.html
In the second case you have to specify both the basis set (GEN) and the
pseudo-potentials.
I guess you can also have such a line command:
#B3LYP/6-31G Opt Pseudo(SDD)
In this case, the 6-31G will be used for light atoms. But you still have
to put the pseudo-potentials for heavy ones.
You can retrieve the well-formatted basis sets and pseudo potentials in
the web site I have just mentioned.
***************************************************************
For Hg (and most transition metals) you will need to use a basis set
modified with an electrostatic core potential (ECP) which basically removes
the core electrons from the atom and replaces them with an empirical
potential. G98 comes with the LANL2DZ basis and ECP built-in. If you want
to use this basis then set your input like the following:
#P RHF/GEN Pseudo=read
comments...
charge multiplicity
molecular specifications
C N 0
6-31+G(d')
****
Hg 0
LANL2DZ
****
Hg 0
LANL2DZ
The important parts are the Gen and Pseudo=read - this tells gaussian to
look at the end of the input file for the basis set (which can be different
for each atom) and the ECP. In the example above I used carbon and
nitrogen, you would put the element symbol for whatever atoms are in your
molecule there. Let me know if this works for you!
ATTACHMENT AT END OF FILE!

******************************************************************
LanL2DZ basis set should be enough as it goes up to atomic number 83 I
have used it for a number of transition metals already and had no
problems.
******************************************************************
According to the Basis Set Order Form, mercury is only available with the
following basis sets:
WTBS
SBKJC VDZ ECP
CRENBL ECP
CRENBS ECP
Stuttgart RLC ECP
Stuttgart RSC ECP
Ahlrichs Coulomb Fitting
http://www.emsl.pnl.gov:2080/forms/basisform.html
They can be used in Gaussian with the GEN keyword. I do not have any
experience with any of these basis sets.

**************************************************************
You've discovered one of the annoying things about calculations involving
elements past chlorine: not all basis sets have been "parameterized" for all
elements. Somewhere near the front of the G98 manual is a table of which
built-in basis sets are defined for which elements.
For your calculations on Hg compounds, your choices are to use one of the
built-in basis sets that is defined for that element, or to use gen and
pseudo=cards to read in a basis set and pseudopotential that is not built
into Gaussian.



****************************************************************
Benjamin J. Moritz                                       home (602) 453-9411
Dept. of Chemistry & Biochemistry                 work (480) 965-8509
Arizona State University                                Mailto:bmoritz@asu.edu
P. O. Box 871604
Tempe, AZ  85287-1604
****************************************************************

"Karma is justice without the satisfaction."
 --=====================_50618335==_.ALT-- --=====================_50618330==_ Content-Type: text/plain; charset="us-ascii" Content-Disposition: attachment; filename="PtCO2CN2-GS~GS~Lanl2DZ-STO3G-OPT.GJF" %chk=PtCO2CN2-LANL2DZ-RHF.chk #P RHF/Gen Pseudo=Read OPT(Calcfc) pop=full gfinput iop(6/7=3) Density=Current SCF=Tight Nosymm Optimize the Ground State of Pt(CO)2(CN)2 at RHF/(LANL2DZ,STO-3G) 0 1 C N,1,R2 Pt,1,R3,2,A3 C,3,R4,1,A4,2,D4,0 C,3,R5,1,A5,4,D5,0 C,3,R6,4,A6,1,D6,0 N,4,R7,3,A7,1,D7,0 O,5,R8,3,A8,1,D8,0 O,6,R9,3,A9,1,D9,0 Variables: R2=1.15108055 R3=1.98976461 R4=1.98976461 R5=2.04407697 R6=2.04407697 R7=1.15108055 R8=1.11956234 R9=1.11956234 A3=178.61942868 A4=89.30938056 A5=86.63735515 A6=86.63735515 A7=178.61942868 A8=177.66388611 A9=177.66388611 D4=179.99793404 D5=180. D6=180. D7=180. D8=0. D9=-0.00125552 O C N 0 STO-3G **** PT 0 LANL2DZ **** PT 0 LANL2DZ --=====================_50618330==_-- From chemistry-request@server.ccl.net Thu Nov 2 12:50:45 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA06165 for ; Thu, 2 Nov 2000 12:50:44 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id JAA00152; Thu, 2 Nov 2000 09:49:37 -0800 (PST) Received: from osman-pc.msi.com(146.202.7.202) by mailhost.msi.com via smap (V2.0) id xma000148; Thu, 2 Nov 00 09:49:16 -0800 Message-Id: <5.0.0.25.0.20001102091401.02bb7eb0@146.202.6.217> X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Thu, 02 Nov 2000 09:15:58 -0600 To: chemistry@server.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, qsar_society@msi.com From: "Osman F. Guner" Subject: 2nd Call for Papers - Pharmacophores Cc: acsmedi@lists.wayne.edu, mol-diversity@listserv.arizona.edu Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_9530924==_.ALT" --=====================_9530924==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Apologies for multiple-list posting... It has been two years since the last big pharmacophore symposium and there= =20 are new developments and success stories out there. We will organize the=20 papers with respect to applications, success stories, new approaches, as=20 well as "creative use of pharmacophores," provided we can populate each=20 category with enough papers. We will have a PC projector at each session;= =20 so don't hold back any of your colorful pharmacophore models. This is a=20 great forum for you to share your experiences with scientists in your=20 field, and benefit from others' experiences at the same time. You are=20 likely to return home with several fresh ideas to apply to your research=20 projects. Besides, first week of April in San Diego?.. can't possibly get= =20 any better than this. Help us make this symposium a memorable event by=20 contributing with your recent work in this area. Thx...Osman ADVANCES IN 3D SEARCHING AND PHARMACOPHORES At Spring ACS meeting in San Diego (April 1-5, 2001) Sponsored by the Chemical Information Division (CINF) Co-sponsored by Division of Medicinal Chemistry (MEDI) and Computers in Chemistry (COMP) The symposium will be on recent advances in 3D searching and pharmacophore= =20 development technologies as well as experiences in using these technologies= =20 in drug discovery and design. Please use the OASys to submit your abstract. You can access the CINF=20 symposia at OASys via http://oasys.acs.org/acs/221nm/cinf/papers/index.cgi.= =20 The deadline for submitting abstracts is November 30th. --- Osman F. G=FCner, Ph.D. Director, Lead Identification & Optimization Molecular Simulations Inc. (858) 799-5341 osman@msi.com http://www.msi.com --=====================_9530924==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Apologies for multiple-list posting...

It has been two years since the last big pharmacophore symposium and there are new developments and success stories out there.  We will organize the papers with respect to applications, success stories, new approaches, as well as "creative use of pharmacophores," provided we can populate each category with enough papers.  We will have a PC projector at each session; so don't hold back any of your colorful pharmacophore models.  This is a great forum for you to share your experiences with scientists in your field, and benefit from others' experiences at the same time.  You are likely to return home with several fresh ideas to apply to your research projects.  Besides, first week of April in San Diego?.. can't possibly get any better than this.  Help us make this symposium a memorable event by contributing with your recent work in this area.  Thx...Osman


ADVANCES IN 3D SEARCHING AND PHARMACOPHORES

At Spring ACS meeting in San Diego (April 1-5, 2001)
Sponsored by the Chemical Information Division (CINF)
Co-sponsored by Division of Medicinal Chemistry (MEDI)
and Computers in Chemistry (COMP)

The symposium will be on recent advances in 3D searching and pharmacophore development technologies as well as experiences in using these technologies in drug discovery and design.

Please use the OASys to submit your abstract. You can access the CINF symposia at OASys via http://oasys.acs.org/acs/221nm/cinf/papers/index.<= a href=3D"http://oasys.acs.org/acs/221nm/cinf/papers/index.cgi" eudora=3D"au= tourl">cgi. The deadline for submitting abstracts is November 30th.


---
Osman F. G=FCner, Ph.D.
Director,  Lead Identification & Optimization
Molecular Simulations Inc.   (858) 799-5341
osman@msi.com        http://www.msi.com --=====================_9530924==_.ALT-- From chemistry-request@server.ccl.net Fri Nov 3 10:58:38 2000 Received: from fcindy13.ncifcrf.gov (fcindy13.NCIFCRF.GOV [129.43.6.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA12292 for ; Fri, 3 Nov 2000 10:58:38 -0500 Received: from localhost (mab@localhost) by fcindy13.ncifcrf.gov (SGI-SGI-8.9.3/8.9.3) with ESMTP id KAA65828; Fri, 3 Nov 2000 10:56:15 -0500 (EST) Date: Fri, 3 Nov 2000 10:56:14 -0500 From: Buyong Ma To: Ramon Garduno cc: CCL POST MSG Subject: Re: CCL:Difficulties using Discover of Biosym In-Reply-To: <200011030136.RAA27040@ce.fis.unam.mx> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The total number of atoms and groups in your list do not include those generated from PBC condition (image atoms and groups). the error message: > error: dimensions for groups must be at least 10125 > Discover must halt. > error: dimensions for atoms must be at least 25302 > Discover must halt. indicates how large the real system is. Ask MSI to get premission downloading new version of discover programm which can handle big system. ================================================================= Buyong Ma, PhD Laboratory of Experimental and Computational Biology National Cancer Institute Frederick, MD 21702, USA Voice (301) 846-6540 E-mail mab@fcindy13.ncifcrf.gov ================================================================= On Thu, 2 Nov 2000, Ramon Garduno wrote: > Dear CCLers: > > I have a problem running a Discover job (BIOSYM-InsightII 95) that I have > been dealing with for about one week, and finally I have given up. > > I would like to hear from more advanced users of this software. I am sure > that the system I want to study does not represent a problem since many > other researchers have used it for larger molecules. > > This is what I have done... > 1) Built a system of one cyclodextrin molecule (146 atoms) and a ibuprofen > molecule (32 atoms) soaked with 2040 water molecules. > 2) This system is held in a cubic box of 40 angstrom per side > 3) I have selected the PCB option and the amber force field. > 4) I have set cutoff = 19.0 cutdis =18.0 and swtdis = 1.5. > 5) The current limits are > total no. atoms 6285 limit 25000 > total no. groups 2037 limit 8000 > total no. residues 2037 limit 7520 > total no. molecules 2037 limit 7500 > total no. bonds 4257 limit 30000 > total no. valence angles 2380 limit 50000 > total no. torsion angles 542 limit 75000 > total no. out of planes 7 limit 7500 > total no. theta*theta angles 0 limit 87500 > total no. excluded atoms 14310 limit 325000 > > However I get these errors which I do not understand....... > > error : too many atoms generated for dimensions > change MXATM to exceed the number of atoms generated > error : too many groups generated for dimensions > change MXGRP to exceed the number of groups generated > error: dimensions for groups must be at least 10125 > Discover must halt. > error: dimensions for atoms must be at least 25302 > Discover must halt. > > > I will appreciate any hints as to how I can fix my problem. > > Much obliged, > > Ramon > -- > > "There are so many ways.... > There is so little time...." > "Hay tantos caminos..... > Pero, hay tan poco tiempo....." > ___________________________________________________________________________ > Dr. Ramon Garduno-Juarez > Research Professor in Biophysics > CENTRO DE CIENCIAS FISICAS | EMAIL: ramon@ce.fis.unam.mx > UNIVERSIDAD NAL. AUTONOMA DE MEXICO | > Apdo. Postal 48-3 | VOICE: +52(5)6227749 ; +52(7)3291749 > 62251 Cuernavaca, Morelos | > MEXICO | FAX: +52(5)6227775 & +52(7)3291775 > ___________________________________EOF ____________________________________ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Nov 3 11:19:39 2000 Received: from iris.iupui.edu (iris.iupui.edu [134.68.220.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA12448 for ; Fri, 3 Nov 2000 11:19:39 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id LAA29885; Fri, 3 Nov 2000 11:19:15 -0500 (EST) Message-ID: Date: 3 Nov 2000 11:33:47 -0500 From: "Boyd" Subject: Emerging Technologies/COMP 2001 To: "Amber list" , "Cache list" , "CHMINF-L" , "MacroModel list" , "MEDI ACS Listserv" , "OSC CCL" , "QSAR & Modelling Society" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Computational Chemists, (Apologies for multiple-list posting.) Next summer, the Computers in Chemistry Division (COMP) will be holding the second annual Symposium on Emerging Technologies. The symposium will be at the American Chemical Society National Meeting, Chicago, Illinois, USA, August 26-30, 2001. A $1000 prize, kindly sponsored by Schrodinger, Inc., will be to be presented for the best talk at the symposium. You are invited to participate. The talks will be evaluated by a Panel of Experts based on the impact the research will have on the future of computational chemistry and allied sciences. The symposium will be ideal for presenting your latest and best methodological advances. To participate, e-mail a 1000-word (text-only) abstract to me no later than March 1, 2001. The talks must be original and not be repeats of talks at other ACS symposia. Sincerely, Don Donald B. Boyd, Ph.D. Organizer, COMP's Symposium on Emerging Technologies Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu COMP http://membership.acs.org/C/COMP/ Schrodinger, Inc. http://www.schroedinger.com/ From chemistry-request@server.ccl.net Fri Nov 3 11:40:22 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA12545 for ; Fri, 3 Nov 2000 11:40:22 -0500 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id LAA15352 for ; Fri, 3 Nov 2000 11:40:06 -0500 (EST) Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id IAA22311 for ; Fri, 3 Nov 2000 08:41:43 -0800 (PST) Received: from unknown(146.202.11.79) by mailhost.msi.com via smap (V2.0) id xma022303; Fri, 3 Nov 00 08:41:38 -0800 Message-Id: <5.0.0.25.2.20001103083230.02c0b8a0@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Fri, 03 Nov 2000 08:35:57 -0800 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: CCL:Difficulties using Discover of Biosym : Images Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Ramon, I believe the problem you are running into, has to do with the way the images are being handled in Discover. I have found some reference to this is an older version of Discover on MSI support's FAQ pages. [ msi.com / User Zone / FAQs / Discover / #6 in the Discover 2.9.x section] I encourage you to contact MSI support to see if this information is still applicable to the version of Discover you are using. Hope this helps! Don Gregory >From: Ramon Garduno >Subject: CCL:Difficulties using Discover of Biosym >To: chemistry@ccl.net (CCL POST MSG) >Date: Thu, 02 Nov 2000 17:36:25 PST >X-Mailer: Elm [revision: 212.2] >Sender: "Computational Chemistry List" > >Dear CCLers: > >I have a problem running a Discover job (BIOSYM-InsightII 95) that I have >been dealing with for about one week, and finally I have given up. > >I would like to hear from more advanced users of this software. I am sure >that the system I want to study does not represent a problem since many >other researchers have used it for larger molecules. > >This is what I have done... >1) Built a system of one cyclodextrin molecule (146 atoms) and a ibuprofen > molecule (32 atoms) soaked with 2040 water molecules. >2) This system is held in a cubic box of 40 angstrom per side >3) I have selected the PCB option and the amber force field. >4) I have set cutoff = 19.0 cutdis =18.0 and swtdis = 1.5. >5) The current limits are >total no. atoms 6285 limit 25000 >total no. groups 2037 limit 8000 >total no. residues 2037 limit 7520 >total no. molecules 2037 limit 7500 >total no. bonds 4257 limit 30000 >total no. valence angles 2380 limit 50000 >total no. torsion angles 542 limit 75000 >total no. out of planes 7 limit 7500 >total no. theta*theta angles 0 limit 87500 >total no. excluded atoms 14310 limit 325000 > >However I get these errors which I do not understand....... > > error : too many atoms generated for dimensions > change MXATM to exceed the number of atoms generated > error : too many groups generated for dimensions > change MXGRP to exceed the number of groups generated > error: dimensions for groups must be at least 10125 > Discover must halt. > error: dimensions for atoms must be at least 25302 > Discover must halt. > > >I will appreciate any hints as to how I can fix my problem. > >Much obliged, > >Ramon >-- Dr. Don Gregory (dgregory@msi.com) CHARMm Product Marketing Manager Molecular Simulations Inc. (http://www.msi.com) 9685 Scranton Rd. San Diego, CA 92121 Office Phone: (858) 799-5331 Mobile Phone: (619) 200-3613 From chemistry-request@server.ccl.net Fri Nov 3 13:56:49 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA13729 for ; Fri, 3 Nov 2000 13:56:49 -0500 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id MAA23689; Fri, 3 Nov 2000 12:56:32 -0600 (CST) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id MAA26078; Fri, 3 Nov 2000 12:56:22 -0600 (CST) Date: Fri, 3 Nov 2000 12:56:22 -0600 (CST) From: TREVOR D POWER To: "Dr. Antonio Buljan" cc: chemistry@server.ccl.net Subject: Re: CCL:Dipole Moment In-Reply-To: <3A02B474.82C98ED6@udec.cl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Antonio, I do not know if this is the BEST methodology (other responses will give you some idea about that) but a good way to do this is to optimize your molecules with correlated methods to give you a very high quality geometry and then perform a single-point calculation with Sadlej's basis set: Sadlej, A. J. Collect. Czech. Chem. Commun. 1988, 53, 1995. (where 1988 is the publication year) whereby you obtain the dipole moments (also quadrupole moments) very accurately when compared to experiment. Some work I was involved in a few years ago, we calculated these types of things for nucleic acid bases: J. Phys. Chem. 1996, 100, 18875. and could only afford MP2 geometry optimizations with 6-31G(d,p) and that actually gave nice results when compared to geometrical details from experiment. You will note that the Pople series of basis sets, whilst good for geometry optimizations, give miserable results for electric properties of molecules. You will, however, find quite a lot of people who seem to "sneek through the cracks" and publish junk results for these types of things. You would be well advised to stick close to Physical Chemistry/Theory type articles. There are a few people who choose to perturb 6-31G (or some variation of this) and they have improved the accuracy of the dipole moment but nowhere near as well as Sadlej's will. I would not personally recommend you do this, but if you are interested in seeing an example of this then I refer you to: Sponer, J.; Hobza, P. J. Phys. Chem. 1994, 98, 3161. Regards, Trevor D. Power Department of Chemistry University of North Texas NT Station, Box 305070 Denton, Texas 76203-5070 tdp0006@unt.edu On Fri, 3 Nov 2000, Dr. Antonio Buljan wrote: > Dear CCLers, > > What is the best methodology to calculate > dipole moments in diatomic molecules? > (for example: CO, LiH, etc.) > > Dr. Antonio Buljan > Departamento de Fisico Quimica > Universidad de Concepcion > Casilla 160-C > CHILE > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Nov 3 14:53:29 2000 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA14015 for ; Fri, 3 Nov 2000 14:53:29 -0500 Received: from iaf.uquebec.ca ([198.168.44.64]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 306 for ; Fri, 3 Nov 2000 14:49:14 -0500 Message-ID: <3A0318B4.C2A0CB1D@iaf.uquebec.ca> Date: Fri, 03 Nov 2000 14:57:40 -0500 From: "Jianhui Wu" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: summary: template, NMR or X-ray Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All, Early this week I asked a general question regarding homology modelling. I received a lot of very helpful respond. I would like to thank Drs. P.I.W. de. Bakker, M.R. Donkey, M. Forster, S. Cross, V. Mathura and J. Gomar for their help. The quality of the crystal struture and the sequence similarity between the target and the templates are key factors to be considered. NMR structure reflect the flexible part of the structure. It is hard to tell whether the model from X-ray or NMR will be better. I intend to use the model to do some database screen and the compounds with top score will be synthesized and subject to biological assay. In other word, the model (and probably me ) have to face the music really soon. As suggested, I will try to build two models (one from NMR, the other one from X-ray) since the sequence similarity between the target and template is about the same in both case. I will use some active compounds as the control in the docking. If nothing active in the end, chemistry guy might ...... . Oops, kind of scaring. Best regards, Yours sincerely, Jian Hui Wu PS: Please find my original question and the responds as follows (text were edited due to broken lines). ***********Original question********************************* > I have a general question regarding homology modelling. I would like to > build a protein model for docking study. This protein have two close > homology proteins (A and B) with their structures solved: A from X-ray > and B from NMR. I wonder which template I should use? or perhaps I should use two of them at the same time? What kind of template will produce better protein model if we try to judge the model by the docking result as well as the biological experimental result. It seems that NMR structure will be more in accord with what is going on in solution. Can we say that model built by template from NMR will give a better result in docking study? Let`s assume the docking method and biological assay method are reasonable here. Any help will be grateful appreciated. **************Responds******************************** (1) "P.I.W. de Bakker" That very much depends on two things: (a) What is the quality of the crystal structure (its resolution)? In comparative modelling people tend to prefer the x-tal structure to the NMR structure. However, if the x-tal structure is, let's say 3.0 A resolution, then the NMR might be a better template. (b) Just as important, what's the similarity of your target sequence to both the NMR and X-ray structure? If your target sequence is much more distant to the Xray structure then too you should use the NMR structure. If your target is an obvious homologue (>50% PID) then take the highest quality template. That you're using the comparative model for docking studies should in this regard not matter. Yours, Paul ***************************************** (2) Mr Donkey Jianhui, First let me start by saying, I have NOT come across anything in the literature that says as a general rule that an NMR struct or X-ray struct will give better homology modeling results. Many modeling studies have been done, using X-ray and NMR structures. >From the homology modeling viewpoint, X-ray has the advantage of only offering 1 structure, whereas NMR structures are deposited in an ensemble of conformers, all of which satisfy the restarings derived from the experiments. So this presents another problem/decision in the homology modeling process - which conformer(s) will you use? or maybe an average structure? As you suggested, you can also use a combination of templates. The most important factor in choosing the templates is the sequence identity; I don't think experimental technique plays any role in this decision. hope this helps - don ************************************************** (3) Mark Forster Dear Jianhui Wu In such a situation you can use two template molecules. Several programs support such a facility (Modeller is one such program). Distance constraints derived from both structures can be used in a single penalty function for optimisation. The relative weights of the constraints from the two structures will depend on the local similarity between the template and query sequence. Mark ******************************************************** (4) Simon Cross Hello, I build homology models of antibodies and use purely crystal structures and loop grafting before minimising. However, if NMR structures were available then I would tend to use them more as it is a more accurate representation in solution, as you have said. The model you build can never be proven to be 100% accurate, so as long as you realise the limitations inherent in the method then it's ok. Why not try to construct two models, one from X-ray, one from NMR and compare the two? If you get a docked structure just from NMR then it will be interesting, as maybe the binding site exists in the 'closed' form in the crystal structure. Any interaction is just a 'possible' so don't try to draw concrete conclusions. Hope this helps, Simon Cross University of Nottingham UK **************************************************** (5) Venkat Mathura hi, if this question is about making just the models than I would say go ahead with template structure determined by X-ray (provided its of high resolution). But, if I am correct, you want to build a multimer. In that case I would suggest build models with both x-ray and NMR templates (do compare the templates itself to understand where exactly the differences are). Then try to dock with both the models (provided if it is not a very tedious process!). The reason for that is X-ray structures is just one, and NMR structures (although bundled , sometimes averaged) of course do represent the solution state. So each has its own benefit. Your aim will be to dock molecules without problem. If both the models (based on X-ray and NMR ) are good, than just X-ray result will be fine. In short, 1. consider X-ray struct resolution 2. consider the xray and nmr struc difference 3. consider xray or nmr struc if multimeric struc is already available (who knows while docking there may be conformational changes, so as a safe bet its better to use similarly docked or multimeric structure) 4. evaluate your models based on both templates 5. which ever you find good will be the one you want 6. if both are good x-ray will be fine, all the best venkat ********************************************* (6) Jerome Gomar Dear Jianhui, Your homology modeling problem can be splitted in two issues : 1/ which reference structure should you choose ? The answer is in the % of sequence homology between your target ( the protein to be modelled) and your template ( protein A and/or B). More precisely, the local sequence homology (calculated on a segment part of the sequence) could give you some indication of structurally conserved regions ( sequence homology is a necessary condition for structural similarity). This % of homology could give you an indication of the weight of the 3D information coming from protein A or B that you need to build the homology model. 2/ What kind of information could you get from NMR ? NMR structures will give you some additional usefull indication on the flexibility of some part of the structure, in the loops for example. If you are performing some docking, this kind of information is important. To my point of view, you should consider the average minimized NMR structure as your template B. Hope this help. Regards Jérôme ********************************************************* E.O.F. From chemistry-request@server.ccl.net Fri Nov 3 17:40:49 2000 Received: from mb1i0.ns.pitt.edu (mb1i0.ns.pitt.edu [136.142.186.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA15640 for ; Fri, 3 Nov 2000 17:40:49 -0500 Received: from recife ("port 2516"@[136.142.153.159]) by pitt.edu (PMDF V5.2-32 #41462) with SMTP id <01JW41DN304Q0054AB@mb1i0.ns.pitt.edu> for chemistry@ccl.net; Fri, 3 Nov 2000 17:40:16 EST Date: Fri, 03 Nov 2000 17:50:30 -0500 From: Gustavo Moura Subject: Semiempirical Magnetic Moments - Summary To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal Dear CCL readers, a few days ago I posted a message asking for information about the semiempirical calculation of magnetic moments. I thank Serguei Patchkovskii and Jens Spanget-Larsen for their answers. Sincerely yours Gustavo Moura gustavo@dumbo.chem.pitt.edu Original Message: Dear CCL readers, I am looking for material (papers, books, WebPages?, etc) describing the semiempirical (CNDO and/or INDO) evaluation of magnetic moment integrals. I already found material describing the semiempirical calculation of electric dipole moments and now I need material describing the evaluation of magnetic moment integrals. I am also interested in knowing about the origin dependence of such semiempirical integrals and how to solve it (are there semiempirical GIAOs?). Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura gustavo@dumbo.chem.pitt.edu Answer #1 (Serguei Patchkovskii): Try: http://www.cobalt.chem.ucalgary.ca/ps/thesis/ It deals with MNDO, but the integrals should be a superset of those you'll encounter in CNDO and INDO. /Serge.P --- Home page: http://www.cobalt.chem.ucalgary.ca/ps/ Answer #2 (Jens Spanget-Larsen): Regarding semiempirical evaluation of magnetic moment integrals, some early applications of "Linderberg's Relation" come to my mind: J. Linderberg: Chem. Phys. Letters 1, 39 (1967) J. Linderberg, J. Michl: J. Am. Chem. Soc. 92, 2619 (1970) S. M. Warnick, J. Michl: J. Am. Chem. Soc. 96, 6280 (1974) E. Dalgaard, J. Linderberg: Int. J. Quantum Chem. 9S, 269 (1975) E. Dalgaard, J. Linderberg: J. Chem. Phys. 65, 692 (1976) A more recent example is J. Spanget-Larsen: Theor. Chem. Acc. 98, 137 (1997) [equation (46) on p. 143]. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=