Hi Yolanda,<br>
<br>
That is a bit of a matter of taste or believe, but probably Yang Ye is
correct that OPLS is among the best choices. However, the Gromos force
fields have proven their value too. The problem with the gmx force
field is that the development has stopped some while ago, it was sort
of abandoned, and it doesn't always give the 'right' behaviour. This
has crossed the mailing list in the past several times. For specific
information, other people will prove more useful...<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 2/3/06, <b class="gmail_sendername">Yang Ye</b> <<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
opls-aa<br><br>YOLANDA SMALL wrote:<br>> Thanks to Daniela, Yang and Tsjerk for a reply...your advice was helpful.<br>><br>> Tsjerk, you were exactly correct, I did have multiple listings of the directive<br>> in my ligand and ions .itp files. But now you raise a point that concerns
<br>> me....why is ffgmx not reliable?<br>><br>> I always check the energies and structures for unusual behavior throughout the<br>> simulations. How does this unreliability manifest itself? Which is the most
<br>> highly recommended forcefield option in the gmx package?<br>><br>> Many thanks,<br>> YAS<br>><br>> On Fri, 03 Feb 2006 09:37:27 +0100, Tsjerk Wassenaar wrote:<br>><br>><br>>> Hi Yolanda,
<br>>><br>>> And then for the solution to your problem... The error in grompp indicates<br>>> that you call the force field defaults directive (ffgmx.itp) several times.<br>>> Probably, the prodrg server has added a statement similar to #include "
<br>>> ffgmx.itp" to the itp files for the ligand and the cofactor. You should<br>>> delete those statements, which will probably solve the error.<br>>><br>>> By the way, the ffgmx force field isn't particularly reliable.
<br>>><br>>> Cheers,<br>>><br>>> Tsjerk<br>>><br>>> On 2/3/06, Yang Ye <<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com</a>> wrote:<br>>><br>>>> Run
GMXRC.xxx according to the shell you are using before running gromacs<br>>>> programs.<br>>>><br>>>> Yang Ye<br>>>><br>>>> -----Original Message-----<br>>>> From: <a href="mailto:gmx-users-bounces@gromacs.org">
gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>]<br>>>> On Behalf Of YOLANDA SMALL<br>>>> Sent: Friday, February 03, 2006 1:12 AM
<br>>>> To: Discussion list for GROMACS users<br>>>> Subject: [gmx-users] Multiple chains, cofactors and ligands<br>>>><br>>>> Dear users,<br>>>><br>>>> I am having a problem with grompp which gives me the following message:
<br>>>> Fatal error: Invalid order for directive defaults, file<br>>>> ""/gromacs-3.2.1/share/top/ffgmx.itp"", line 4<br>>>><br>>>> My simulation details:<br>>>> An enzyme with 2 chains, 2 cofactors and 2 ligands in a 115 Angstrom box
<br>>>> of<br>>>> SPC<br>>>> waters. The total system size is 150872 atoms. Each chain has a separate<br>>>> .itp<br>>>> file created with pdb2gmx. Each cofactor and ligand has an .itp file
<br>>>> created<br>>>> with PRODRG. The files are joined in the following topology file:<br>>>><br>>>> ; Include forcefield parameters<br>>>> #include "ffgmx.itp"<br>
>>><br>>>> ; Include chain topologies<br>>>> #include "chain_A.itp"<br>>>> #include "chain_B.itp"<br>>>> #include "cofactor_A.itp"<br>>>> #include "cofactor_B.itp"
<br>>>> #include "ligand_A.itp"<br>>>> #include "ligand_B.itp"<br>>>> #include "Na.itp"<br>>>><br>>>> ; Include water topology<br>>>> #include "
spc.itp"<br>>>><br>>>> ; Include generic topology for ions<br>>>> #include "ions.itp"<br>>>><br>>>> [ system ]<br>>>> ; Name<br>>>> 2 COMPLEXED WITH (Ligand)
<br>>>><br>>>> [ molecules ]<br>>>> ; Compound #mols<br>>>> Protein_A 1<br>>>> Protein_B 1<br>>>> SOL 346<br>>>> COF_A 1
<br>>>> COF_B 1<br>>>> LIG_A 1<br>>>> LIG_B 1<br>>>> NA 1<br>>>> SOL 47872<br>>>><br>>>> The problem:
<br>>>> I only get this message when the topology of the cofactor and ligand are<br>>>> included. When I run the simulation on the protein chains only without<br>>>> the<br>>>> ligand and cofactor, it runs just fine. I double-checked the topology of
<br>>>> the<br>>>> ligand and cofactor and I don't see any errors. Do I need to change the<br>>>> defaults in the following ffgmx.itp file to get this to work???? (The<br>>>> error<br>>>> message points to line 4 of this file) If so, what should I change the
<br>>>> defaults to?<br>>>><br>>>> #define _FF_GROMACS<br>>>> #define _FF_GROMACS1<br>>>><br>>>> [ defaults ]<br>>>>
;
nbfunc comb-rule
gen-pairs fudgeLJ fudgeQQ<br>>>>
1
1
no 1.0
1.0<br>>>><br>>>> #include "ffgmxnb.itp"<br>>>> #include "ffgmxbon.itp"<br>>>><br>>>> Thanks in advance for your help,<br>>>> YAS<br>>>> _______________________________________________
<br>>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>>>> Please don't post (un)subscribe requests to the list. Use the<br>>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>>> Can't post? Read
<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>>>><br>>>><br>>>> _______________________________________________<br>>>> gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>>> Please don't post (un)subscribe requests to the list. Use the
<br>>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</a><br>>>><br>>>><br>>><br>>> --<br>>><br>>> Tsjerk A. Wassenaar, M.Sc.<br>>> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>>> Dept. of Biophysical Chemistry
<br>>> University of Groningen<br>>> Nijenborgh 4<br>>> 9747AG Groningen, The Netherlands<br>>> +31 50 363 4336<br>>> Hi Yolanda,<br>>><br>>> And then for the solution to your problem... The error in grompp
<br>>> indicates that you call the force field defaults directive (ffgmx.itp)<br>>> several times. Probably, the prodrg server has added a statement<br>>> similar to #include "ffgmx.itp" to the itp files for the ligand and the
<br>>> cofactor. You should delete those statements, which will probably solve<br>>> the error.<br>>><br>>> By the way, the ffgmx force field isn't particularly reliable.<br>>><br>>> Cheers,
<br>>><br>>> TsjerkOn 2/3/06, Yang Ye <<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com</a>> wrote:<br>>> Run GMXRC.xxx according to the shell you are using before running<br>
>><br>> gromacsprograms.Yang Ye-----Original Message-----From:<br>> <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a><br>><br>>> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">
gmx-users-bounces@gromacs.org</a>]On Behalf Of YOLANDA SMALLSent: Friday,<br>>><br>> February 03, 2006 1:12 AMTo: Discussion list for GROMACS usersSubject:<br>> [gmx-users] Multiple chains, cofactors and ligands
<br>><br>>> Dear users,I am having a problem with grompp which gives me the following<br>>><br>> message:Fatal error: Invalid order for directive defaults,<br>> file""/gromacs-3.2.1/share/top/ffgmx.itp"", line 4
<br>><br>>> My simulation details:An enzyme with 2 chains, 2 cofactors and 2 ligands in a<br>>><br>> 115 Angstrom box ofSPCwaters. The total system size is 150872 atoms. Each<br>> chain has a separate.itpfile
created with pdb2gmx. Each cofactor and ligand has<br>> an .itp file created<br>><br>>> with PRODRG. The files are joined in the following topology file:; Include<br>>><br>> forcefield parameters#include "
ffgmx.itp"; Include chain topologies#include<br>> "chain_A.itp"#include "chain_B.itp"<br>><br>>> #include "cofactor_A.itp"#include "cofactor_B.itp"#include<br>>>
<br>> "ligand_A.itp"#include "ligand_B.itp"#include "Na.itp"; Include water<br>> topology#include "<br>><br>>> spc.itp"; Include generic topology for ions#include "
ions.itp"[ system ];<br>>><br>> Name2 COMPLEXED WITH (Ligand)[ molecules ]; Compound #molsProtein_A<br>> 1<br>><br>>>
Protein_B
1SOL
346COF_A
1COF_B<br>>><br>>
1LIG_A
1LIG_B
1NA 1SOL<br>> 47872The problem:I only get this message when the topology of the cofactor<br>> and ligand are<br>><br>>> included. When I run the simulation on the protein chains only without
<br>>><br>> theligand and cofactor, it runs just fine. I double-checked the topology<br>> oftheligand and cofactor and I don't see any errors. Do I need to change the<br>><br>>> defaults in the following
ffgmx.itp file to get this to work???? (The<br>>><br>> errormessage points to line 4 of this file) If so, what should I change<br>> thedefaults to?#define _FF_GROMACS#define _FF_GROMACS1<br>><br>>> [ defaults ];
<br>>> nbfunc comb-rule<br>>> gen-pairs fudgeLJ fudgeQQ 1<br>>> 1<br>>> no 1.0<br>>> 1.0#include "ffgmxnb.itp"#include "ffgmxbon.itp"Thanks in advance for your
<br>>><br>> help,YAS_______________________________________________gmx-users mailing list<br>><br>><br>>> gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease<br>>><br>> don't post (un)subscribe requests to the list. Use thewww interface or send it
<br>> to<br>><br>>> <a href="mailto:gmx-users-request@gromacs.org.Can">gmx-users-request@gromacs.org.Can</a>'t post? Read<br>>><br>> <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</a><br>><br>>> _______________________________________________gmx-users mailing list<br>>><br>> gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users<br>><br>>> Please don't post (un)subscribe requests to the list. Use thewww interface or
<br>>><br>> send it to <a href="mailto:gmx-users-request@gromacs.org.Can">gmx-users-request@gromacs.org.Can</a>'t post? Read<br>><br>>> <a href="http://www.gromacs.org/mailing_lists/users.php--">http://www.gromacs.org/mailing_lists/users.php--
</a> Tsjerk A. Wassenaar,<br>>><br>> M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of<br>> Biophysical Chemistry<br>><br>>> University of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363
<br>>><br>> 4336<br>><br>>> _______________________________________________<br>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please don't post (un)subscribe requests to the list. Use the<br>>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>>><br>><br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br>><br><br>--<br>/Regards,/<br>Yang Ye<br>/Computational Biology Lab<br>
School of Biological Sciences<br>Nanyang Technological University<br>Singapore<br>Tel: 6316-2884<br>/<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote>
</div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands
<br>+31 50 363 4336<br>