<div class="gmail_quote"><div>I have my solution here too, I merged the tip3p files in one that is working for any situation (see the file in attach, they are part of my acpypi distribution anyway).</div><div> </div><div>But because of this post, I was reviewing my *.itp and found that we now have _FF_CHARMM in, e.g., tip3p.itp and spc.itp, but not in spce.itp, why not? Was it forgotten? Anyone would kindly know something about it?</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Alan</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
Jack Shultz wrote:<br>
> Hi all,<br>
><br>
> I think I'm having a problem with the water models. Clearly ther are<br>
> differences in these tip3p models. I can rename the ffamber_tip3p<br>
> files to overwrite existing tip3p files. I don't want to do that<br>
> because I want the option of choosing the amber ones at run-time.<br>
> pdb2gmx does not accept a request for<br>
> -water ffamber_tip3p or -water amber_tip3p<br>
><br>
<br>
The only way I have found to use the ffamber_tip3p is to manually modify the<br>
topol.top after pdb2gmx (i.e., vi or sed), since the Amber force fields are not<br>
standard within Gromacs. I suppose you could somehow modify the pdb2gmx code to<br>
accept different options, but it's probably a lot easier to replace the text in<br>
the post-pdb2gmx topology yourself.<br>
<br>
-Justin<br>
<br>
> Are these the only options I can use?<br>
> -water enum spc Water model to use: with GROMOS we recommend<br>
> SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c<br>
><br>
> $ ls -l *tip3* *spc*<br>
> -rwx------+ 1 jshultz None 1377 Mar 17 11:22 Copy of tip3p.itp<br>
> -rwx------+ 1 jshultz None 106028 Feb 27 18:46 ffamber_tip3p.gro<br>
> -rwx------+ 1 jshultz None 638 Feb 27 18:46 ffamber_tip3p.itp<br>
> -rwx------+ 1 jshultz None 638 Feb 27 18:46 ffamber_tip3p_heavy.itp<br>
> -rwx------+ 1 jshultz None 36 Mar 17 11:21 flexspc.itp<br>
> -rwx------+ 1 jshultz None 37 Mar 17 11:22 flexspce.itp<br>
> -rwx------+ 1 jshultz None 1402 Mar 17 11:22 spc.itp<br>
> -rwx------+ 1 jshultz None 29266 Mar 24 07:40 spc216.gro<br>
> -rwx------+ 1 jshultz None 1142 Mar 17 11:22 spce.itp<br>
> -rwx------+ 1 jshultz None 106028 Feb 27 18:46 tip3p.gro<br>
> -rwx------+ 1 jshultz None 1377 Mar 24 07:40 tip3p.itp<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 30 Mar 2009 11:31:29 +0530<br>
From: nitu sharma <<a href="mailto:sharmanitu35@gmail.com">sharmanitu35@gmail.com</a>><br>
Subject: [gmx-users] grompp error in running simulation of lipid<br>
bilayer<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:5fe39aa90903292301vea30bb9kdb79cebc01b98e11@mail.gmail.com">5fe39aa90903292301vea30bb9kdb79cebc01b98e11@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear all ,<br>
<br>
<br>
I am trying to do simulation of DMPC lipid bilayer<br>
for this I have made topology file with the help of teleman website by<br>
downloading two file -lipid.itp &dmpc.itp . But when I run the grompp for<br>
energy minimisation I am getting error like this -<br>
<br>
Program grompp, VERSION 4.0.3<br>
Source code file: topio.c, line: 430<br>
<br>
Fatal error:<br>
Syntax error - File lipid.itp, line 9<br>
Last line read:<br>
'1 1'<br>
Found a second defaults directive.<br>
<br>
my command line like this- [nitu@localhost dmpc1tap]$ grompp -f em.mdp -p<br>
dmpc.top -c dmpc-solvated.pdb -o dmpc-em.tpr<br>
If anyone know about this please help me in solving this problem .<br>
<br>
its very useful for me.<br>
<br>
thank you very much in advance.<br>
<br>
Nitu Sharma<br>
School Of life sciences<br>
Jawaherlal Nehru University<br>
New Delhi, India<br>
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Message: 7<br>
Date: Mon, 30 Mar 2009 11:36:53 +0530<br>
From: Pawan Kumar <<a href="mailto:pawan.chinari@gmail.com">pawan.chinari@gmail.com</a>><br>
Subject: Re: [gmx-users] grompp error in running simulation of lipid<br>
bilayer<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:143b0c640903292306y6d89c0adm96a27c87cd47442e@mail.gmail.com">143b0c640903292306y6d89c0adm96a27c87cd47442e@mail.gmail.com</a>><br>
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<br>
Hi,<br>
<br>
Greetings from Pawan.<br>
Edit your lipid.itp file.<br>
Comment or remove the lines :<br>
[default]<br>
1 1<br>
<br>
Then grompp will work..<br>
<br>
Regards,<br>
Pawan<br>
<br>
2009/3/30 nitu sharma <<a href="mailto:sharmanitu35@gmail.com">sharmanitu35@gmail.com</a>><br>
<br>
> Dear all ,<br>
><br>
><br>
> I am trying to do simulation of DMPC lipid<br>
> bilayer for this I have made topology file with the help of teleman<br>
> website by downloading two file -lipid.itp &dmpc.itp . But when I run the<br>
> grompp for energy minimisation I am getting error like this -<br>
><br>
> Program grompp, VERSION 4.0.3<br>
> Source code file: topio.c, line: 430<br>
><br>
> Fatal error:<br>
> Syntax error - File lipid.itp, line 9<br>
> Last line read:<br>
> '1 1'<br>
> Found a second defaults directive.<br>
><br>
> my command line like this- [nitu@localhost dmpc1tap]$ grompp -f em.mdp -p<br>
> dmpc.top -c dmpc-solvated.pdb -o dmpc-em.tpr<br>
> If anyone know about this please help me in solving this problem .<br>
><br>
> its very useful for me.<br>
><br>
> thank you very much in advance.<br>
><br>
> Nitu Sharma<br>
> School Of life sciences<br>
> Jawaherlal Nehru University<br>
> New Delhi, India<br>
><br>
><br>
><br>
><br>
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******************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>