From owner-chemistry@ccl.net Wed Dec 16 00:34:01 2009 From: "zjxu zjxu.:.mail.shcnc.ac.cn" To: CCL Subject: CCL:G: zinc parameter for gaff in QM/MM(gaussian) Message-Id: <-40922-091216002632-8912-CJaga5izG+EO1pUOXvtSPQ#server.ccl.net> X-Original-From: zjxu Content-Type: multipart/alternative; boundary="------------030201070008040107000006" Date: Wed, 16 Dec 2009 13:26:48 +0800 MIME-Version: 1.0 Sent to CCL by: zjxu [zjxu . mail.shcnc.ac.cn] This is a multi-part message in MIME format. --------------030201070008040107000006 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: 8bit Mahmoud A. A. Ibrahim m.ibrahim],[compchem.net 写道: > Dear Zhijan > Here is the Zinc ion parameters; sigma= 1.70 and epsion=0.67 > Sorry, due to the copyrights, I couldn't send you the original paper. > I am working on Zinc ion, I found the implemented Zinc ion parameters > in AMBER gives better results in MM simulation. But, you shouldn't > care becuase you are running QM/MM in which Zinc ion will be involved > in the QM part. > Sincerely; > M. Ibrahim > > On Mon, Dec 14, 2009 at 1:40 PM, Zhi Jian Xu zjxu.%a%.mail.shcnc.ac.cn > > wrote: > > > Sent to CCL by: "Zhi Jian Xu" [zjxu{:}mail.shcnc.ac.cn > ] > Dear CCLers, > I need the zinc ion(Zn2+) parameters for gaff(generalized amber > force field) in QM/MM computation using gaussian. I find someone > using the parameters > from : Stote, R. H. and M. Karplus (1995). > "Zinc binding in proteins and solution: a simple but accurate > nonbonded representation." Proteins 23(1): 12-31. Howerver, I did > not have the permission to download the full text. So I am very > appreciate for who could provide the parameters or the full txt. > Thanks in advance! > > XU Zhijian > > > > -= This is automatically added to each message by the mailing > script =- > > > > E-mail to subscribers: CHEMISTRY%a%ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST%a%ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim%a%compchem.net > Website: www.compchem.net > Fax No.: +20862342601 Dear Ibrahim, Thans very much for the parameters and your kind suggestions, that really helps. Xu ZhiJian --------------030201070008040107000006 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: 8bit Mahmoud A. A. Ibrahim m.ibrahim],[compchem.net 写道:
Dear Zhijan
Here is the Zinc ion parameters; sigma= 1.70 and epsion=0.67
Sorry, due to the copyrights, I couldn't send you the original paper.
I am working on Zinc ion, I found the implemented Zinc ion parameters in AMBER gives better results in MM simulation. But, you shouldn't care becuase you are running QM/MM in which Zinc ion will be involved in the QM part.
Sincerely;
M. Ibrahim

On Mon, Dec 14, 2009 at 1:40 PM, Zhi Jian Xu zjxu.%a%.mail.shcnc.ac.cn <owner-chemistry%a%ccl.net> wrote:

Sent to CCL by: "Zhi Jian Xu" [zjxu{:}mail.shcnc.ac.cn]
Dear CCLers,
I need the zinc ion(Zn2+) parameters for gaff(generalized amber force field) in QM/MM computation using gaussian. I find someone using the parameters > from : Stote, R. H. and M. Karplus (1995). "Zinc binding in proteins and solution: a simple but accurate nonbonded representation." Proteins 23(1): 12-31. Howerver, I did not have the permission to download the full text. So I am very appreciate for who could provide the parameters or the full txt.
Thanks in advance!

XU Zhijian





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--
                 Mahmoud A. A. Ibrahim        
                      Current Address
                7.05, School of Chemistry,
             The University of Manchester,
        Oxford Road, Manchester, M13 9PL,
                      United Kingdom.

                       Home Address
                 Chemistry Department,
                    Faculty of Science,
                       Minia University,
                          Minia 61519,
                               Egypt.

                    Contact Information
          Email: m.ibrahim%a%compchem.net
             Website: www.compchem.net
                  Fax No.: +20862342601
Dear Ibrahim,
Thans very much for the parameters and your kind suggestions, that really helps.

Xu ZhiJian --------------030201070008040107000006-- From owner-chemistry@ccl.net Wed Dec 16 03:35:00 2009 From: "andras.borosy-.-givaudan.com" To: CCL Subject: CCL: help with liquid density prediction Message-Id: <-40923-091216032710-3866-ZbkFe/8ZcJbPugo9kFNaLg]*[server.ccl.net> X-Original-From: andras.borosy^givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 002B6F8BC125768E_=" Date: Wed, 16 Dec 2009 08:54:27 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy- -givaudan.com This is a multipart message in MIME format. --=_alternative 002B6F8BC125768E_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Lily, I think COSMOTherm is pretty good for this purpose: http://www.cosmologic.de/index.php You may find references at this homepage. Best wishes, Andr=E1s Borosy "Chunhui Li baotogo2004[*]gmail.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com() ccl.net 15.12.2009 16:55 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: help with liquid density prediction Sent to CCL by: "Chunhui Li" [baotogo2004]-[gmail.com] Dear All, I am trying to predict density for pure organic liquids. I wonder what=20 software (Prefer free) are available for quick and hopefully reliable=20 predictions. Information on review papers are also highly appreciated! Thanks in advance! Lily -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 002B6F8BC125768E_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear  Lily,

I think COSMOTherm is pretty good for this purpose:

http://www.cosmologic.de/index.php

You may find references at this home= page.

Best wishes,

Andr=E1s Borosy




"Chunhui Li baot= ogo2004[*]gmail.com" <owner-chemistry() ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com() ccl.net

15.12.2009 16:55
Please respond to
"CCL Subscribers" <chemistry() ccl.net>
To
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Subject
CCL: help with liquid density predic= tion






Sent to CCL by: "Chunhui  Li" [baotogo2004]-[gmail.com]
Dear All,

I am trying to predict density for pure organic liquids. I wonder what software (Prefer free) are available for quick and hopefully reliable predi= ctions. Information on review papers are also highly appreciated!

Thanks in advance!

Lily



-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
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--=_alternative 002B6F8BC125768E_=-- From owner-chemistry@ccl.net Wed Dec 16 08:04:00 2009 From: "rocky walden rocky.walden19*|*gmail.com" To: CCL Subject: CCL: Needed your expertise guidance Message-Id: <-40924-091216080255-25255-KIOz1CjwtzHKBtg7Z07rEw(-)server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=001485f99caa625a07047ad81fd9 Date: Wed, 16 Dec 2009 18:32:44 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19,,gmail.com] --001485f99caa625a07047ad81fd9 Content-Type: text/plain; charset=ISO-8859-1 Dear Guys, I am planning to validate the Force fields data sets provided in our ccl.net webpages. I am very new to molecular modeling and planning to start learning while working form scratch starting at force fields. can u please mention me what is the specific hardware requirements, software, and i need the work up manual and how to approach the problem My system hardware configuration is Windows XP Service pack 2, Intel 3.6GHz processor and 1 GB Ram, 160GB HDD. I can also update my system software to Ubuntu, RedHat Linux Enterprise edition and Open solaris if needed. Thanks you in your time. Looking for your expertise suggestion. Sincerely, --001485f99caa625a07047ad81fd9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Guys,
=A0 I am planning to validate the Force fields data sets prov= ided in our ccl.net webpages.
I am very n= ew to molecular modeling and planning to start learning while working form = scratch starting at force fields.
can u please mention me what is the specific hardware requirements, software, and i need the work up manual and how to approach the problem
= My system hardware configuration is Windows XP Service pack 2, Intel 3.6GHz= processor and 1 GB Ram, 160GB HDD.
I can also update my system software to Ubuntu, RedHat Linux Enterprise edi= tion and Open solaris if needed.

Thanks you in your time.

Loo= king for your expertise suggestion.

Sincerely, --001485f99caa625a07047ad81fd9-- From owner-chemistry@ccl.net Wed Dec 16 09:28:01 2009 From: "Andreas Bick andreas.bick]=[scienomics.com" To: CCL Subject: CCL: help with liquid density prediction Message-Id: <-40925-091216083708-9224-vDpx8FKaL3zOS5txcu0HxQ^server.ccl.net> X-Original-From: Andreas Bick Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 16 Dec 2009 13:55:47 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Bick [andreas.bick,,scienomics.com] Dear Lily, an NPT molecular dynamics simulation, for example with the LAMMPS free MD code (http://lammps.sandia.gov/) and an appropriate force field could help you in this case. Best regards Andreas > Sent to CCL by: "Chunhui Li" [baotogo2004]-[gmail.com] > Dear All, > > I am trying to predict density for pure organic liquids. I wonder what software (Prefer free) are available for quick and hopefully reliable predictions. Information on review papers are also highly appreciated! > > Thanks in advance! > > Lily> > > -- Dr. Andreas Bick Scienomics SARL Sales and Marketing phone: +492311385847 mobile: +4916096873623 From owner-chemistry@ccl.net Wed Dec 16 11:27:01 2009 From: "John McKelvey jmmckel=gmail.com" To: CCL Subject: CCL: Needed your expertise guidance Message-Id: <-40926-091216110444-21904-USeG1b40azQofaGIUdny1Q/./server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 16 Dec 2009 11:04:33 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel**gmail.com] I would comment that if you are considering RH Enterprise to use its almost equivalent, free CENTOS 5.4 (32 or 64 bit) John Mckelvey On Wed, Dec 16, 2009 at 8:02 AM, rocky walden rocky.walden19*|*gmail.com wrote: > Dear Guys, > =A0 I am planning to validate the Force fields data sets provided in our > ccl.net webpages. > I am very new to molecular modeling and planning to start learning while > working form scratch starting at force fields. > can u please mention me what is the specific hardware requirements, > software, and i need the work up manual and how to approach the problem > My system hardware configuration is Windows XP Service pack 2, Intel 3.6G= Hz > processor and 1 GB Ram, 160GB HDD. > I can also update my system software to Ubuntu, RedHat Linux Enterprise > edition and Open solaris if needed. > > Thanks you in your time. > > Looking for your expertise suggestion. > > Sincerely, --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel|a|gmail.com From owner-chemistry@ccl.net Wed Dec 16 13:44:00 2009 From: "Bill Ross ross(~)cgl.ucsf.edu" To: CCL Subject: CCL: zinc parameter for gaff in QM/MM(gaussian) Message-Id: <-40927-091216132151-28549-aNFWrOSxLbTqfvTpwaXihg:_:server.ccl.net> X-Original-From: Bill Ross Date: Wed, 16 Dec 2009 09:51:30 -0800 (PST) Sent to CCL by: Bill Ross [ross^^cgl.ucsf.edu] > Here is the Zinc ion parameters; sigma= 1.70 and epsion=0.67 I believe that sigma is different from R* used by amber. Here is some discussion of ion param types, but it doesn't mention the sigma convention: http://ambermd.org/Questions/vdw.html By the way, has anyone seen "Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements" http://pubs.acs.org/doi/abs/10.1021/jp0765392 They claim, "These errors arise from an ad hoc adaptation of 舚vist's cation parameters." It seems their understanding of the combining rules used by different force fields is flawed, in that this was used in adapting Aqvist to Amber. On the other hand, they claim to fix observed problems in simulations, so that is interesting. Here is some discussion of the conversion of Aqvist params for Amber: http://pubs.acs.org/doi/abs/10.1021/j100084a050 Bill From owner-chemistry@ccl.net Wed Dec 16 14:19:01 2009 From: "Mark Onyango mark.onyango!A!tg.fh-giessen.de" To: CCL Subject: CCL:G: Optimization of the excited Lb state from Indole Message-Id: <-40928-091216101605-8459-c7YHq2x+tZmx3E9r2fj8rA * server.ccl.net> X-Original-From: "Mark Onyango" Date: Wed, 16 Dec 2009 10:16:01 -0500 Sent to CCL by: "Mark Onyango" [mark.onyango_._tg.fh-giessen.de] Hi, I am trying to optimize the excited Lb state from Indole with the help of Gaussian 09. My Route Section is as follows: # opt=tight td=(singlets,nstates=6,root=3) rcam-b3lyp/aug-cc-pvdz maxdisk=40GB geom=connectivity density=current test Whenever I adjust the root keyword for the appropiate state, derived from a previous try to optimize this state, the order of the states changes again making it almost impossible to optimize the Lb state. Do you have any tricks or is this just luck? I have also tried optimizing the Lb with RI-CC2 first and using the geometry for the job in Gaussian with no success. Thanks in advance. Regards, Mark Onyango (mark.onyango###tg.fh-giessen.de) From owner-chemistry@ccl.net Wed Dec 16 14:59:01 2009 From: "Vincent Leroux vincent.leroux[-]loria.fr" To: CCL Subject: CCL: Needed your expertise guidance Message-Id: <-40929-091216133235-29274-OAQXR8xtvmLjG3w+oUwkng||server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 16 Dec 2009 18:36:54 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux|loria.fr] As for RHEL variants, I would suggest an even better alternative IMHO: Scientific Linux https://www.scientificlinux.org/ Rocky: you should add some RAM and another hard disk to beef up your computer. Serious scientific computations do need a lot of space. And Linux. If you plan to do some modeling, consider at least a entry-level dedicated graphic card if you do not have one already. nVidia GPUs have better Linux support. VL John McKelvey jmmckel=gmail.com a 閏rit : > Sent to CCL by: John McKelvey [jmmckel**gmail.com] > I would comment that if you are considering RH Enterprise to use its > almost equivalent, free CENTOS 5.4 (32 or 64 bit) > > John Mckelvey > > On Wed, Dec 16, 2009 at 8:02 AM, rocky walden > rocky.walden19*|*gmail.com wrote: >> Dear Guys, >> I am planning to validate the Force fields data sets provided in our >> ccl.net webpages. >> I am very new to molecular modeling and planning to start learning while >> working form scratch starting at force fields. >> can u please mention me what is the specific hardware requirements, >> software, and i need the work up manual and how to approach the problem >> My system hardware configuration is Windows XP Service pack 2, Intel 3.6GHz >> processor and 1 GB Ram, 160GB HDD. >> I can also update my system software to Ubuntu, RedHat Linux Enterprise >> edition and Open solaris if needed. >> >> Thanks you in your time. >> >> Looking for your expertise suggestion. >> >> Sincerely, > > > From owner-chemistry@ccl.net Wed Dec 16 15:29:01 2009 From: "AHMAD IRFAN irfaahmad=-=gmail.com" To: CCL Subject: CCL: softwares for plasma modeling Message-Id: <-40930-091216140926-10551-2MTQrrCjPpMNMDctfVFAzQ^server.ccl.net> X-Original-From: "AHMAD IRFAN" Date: Wed, 16 Dec 2009 14:09:22 -0500 Sent to CCL by: "AHMAD IRFAN" [irfaahmad\a/gmail.com] Hi scientists I want to know about the softwares that can calculate the thermodynamic properties and transport properties of plasma. I know one of the software for plasma modeling which is Fluent with PLASMATOR for different plasma properties. Tell me other softwares which can help me From owner-chemistry@ccl.net Wed Dec 16 22:00:00 2009 From: "zjxu zjxu]*[mail.shcnc.ac.cn" To: CCL Subject: CCL: zinc parameter for gaff in QM/MM(gaussian) Message-Id: <-40931-091216211441-9526-RuevA3fbAOXR1V3c5MO9Hg-.-server.ccl.net> X-Original-From: zjxu Content-Type: multipart/alternative; boundary="------------040004030204070808030907" Date: Thu, 17 Dec 2009 10:14:57 +0800 MIME-Version: 1.0 Sent to CCL by: zjxu [zjxu%mail.shcnc.ac.cn] This is a multi-part message in MIME format. --------------040004030204070808030907 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: 8bit Bill Ross ross(~)cgl.ucsf.edu 写道: > Sent to CCL by: Bill Ross [ross^^cgl.ucsf.edu] > >> Here is the Zinc ion parameters; sigma= 1.70 and epsion=0.67 >> > > I believe that sigma is different from R* used by amber. Here > is some discussion of ion param types, but it doesn't mention > the sigma convention: > > http://ambermd.org/Questions/vdw.html > > By the way, has anyone seen "Parameters of Monovalent Ions > in the AMBER-99 Forcefield: Assessment of Inaccuracies and > Proposed Improvements" http://pubs.acs.org/doi/abs/10.1021/jp0765392 > They claim, "These errors arise from an ad hoc adaptation of 舚vist's > cation parameters." It seems their understanding of the > combining rules used by different force fields is flawed, > in that this was used in adapting Aqvist to Amber. On the other > hand, they claim to fix observed problems in simulations, so that > is interesting. > > Here is some discussion of the conversion of Aqvist params for Amber: > http://pubs.acs.org/doi/abs/10.1021/j100084a050 > > Bill> > > > > Bill, Thanks for your response. frankly speaking, I am a little confuesd now. I will read the reference that you provided. In the MM experience(gromacs and amber), I was alerted that it's dangerouse to combine the parameters from diffent force field together. I am not sure how big the difference will be. zjxu --------------040004030204070808030907 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: 8bit Bill Ross ross(~)cgl.ucsf.edu 写道: 
Sent to CCL by: Bill Ross [ross^^cgl.ucsf.edu]
  
Here is the Zinc ion parameters; sigma= 1.70 and epsion=0.67
    

I believe that sigma is different from R* used by amber. Here
is some discussion of ion param types, but it doesn't mention
the sigma convention:

  http://ambermd.org/Questions/vdw.html

By the way, has anyone seen "Parameters of Monovalent Ions 
in the AMBER-99 Forcefield: Assessment of Inaccuracies and 
Proposed Improvements" http://pubs.acs.org/doi/abs/10.1021/jp0765392
They claim, "These errors arise from an ad hoc adaptation of 舚vist's 
cation parameters." It seems their understanding of the 
combining rules used by different force fields is flawed,
in that this was used in adapting Aqvist to Amber. On the other
hand, they claim to fix observed problems in simulations, so that
is interesting.

Here is some discussion of the conversion of Aqvist params for Amber:
http://pubs.acs.org/doi/abs/10.1021/j100084a050

BillE-mail to subscribers: CHEMISTRY_+_ccl.net or use:
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Bill,
Thanks for your response.
frankly speaking, I am a little confuesd now. I will read the reference that you provided. In the MM experience(gromacs and amber), I was alerted that it's dangerouse to combine the parameters from diffent force field together. I am not sure how big the difference will be.

zjxu
 --------------040004030204070808030907--