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).
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? Cheers, Alan > > Jack Shultz wrote: > > Hi all, > > > > I think I'm having a problem with the water models. Clearly ther are > > differences in these tip3p models. I can rename the ffamber_tip3p > > files to overwrite existing tip3p files. I don't want to do that > > because I want the option of choosing the amber ones at run-time. > > pdb2gmx does not accept a request for > > -water ffamber_tip3p or -water amber_tip3p > > > > The only way I have found to use the ffamber_tip3p is to manually modify > the > topol.top after pdb2gmx (i.e., vi or sed), since the Amber force fields are > not > standard within Gromacs. I suppose you could somehow modify the pdb2gmx > code to > accept different options, but it's probably a lot easier to replace the > text in > the post-pdb2gmx topology yourself. > > -Justin > > > Are these the only options I can use? > > -water enum spc Water model to use: with GROMOS we > recommend > > SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c > > > > $ ls -l *tip3* *spc* > > -rwx------+ 1 jshultz None 1377 Mar 17 11:22 Copy of tip3p.itp > > -rwx------+ 1 jshultz None 106028 Feb 27 18:46 ffamber_tip3p.gro > > -rwx------+ 1 jshultz None 638 Feb 27 18:46 ffamber_tip3p.itp > > -rwx------+ 1 jshultz None 638 Feb 27 18:46 ffamber_tip3p_heavy.itp > > -rwx------+ 1 jshultz None 36 Mar 17 11:21 flexspc.itp > > -rwx------+ 1 jshultz None 37 Mar 17 11:22 flexspce.itp > > -rwx------+ 1 jshultz None 1402 Mar 17 11:22 spc.itp > > -rwx------+ 1 jshultz None 29266 Mar 24 07:40 spc216.gro > > -rwx------+ 1 jshultz None 1142 Mar 17 11:22 spce.itp > > -rwx------+ 1 jshultz None 106028 Feb 27 18:46 tip3p.gro > > -rwx------+ 1 jshultz None 1377 Mar 24 07:40 tip3p.itp > > > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Mon, 30 Mar 2009 11:31:29 +0530 > From: nitu sharma <sharmanit...@gmail.com> > Subject: [gmx-users] grompp error in running simulation of lipid > bilayer > To: gmx-users@gromacs.org > Message-ID: > <5fe39aa90903292301vea30bb9kdb79cebc01b98...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all , > > > I am trying to do simulation of DMPC lipid bilayer > for this I have made topology file with the help of teleman website by > downloading two file -lipid.itp &dmpc.itp . But when I run the grompp for > energy minimisation I am getting error like this - > > Program grompp, VERSION 4.0.3 > Source code file: topio.c, line: 430 > > Fatal error: > Syntax error - File lipid.itp, line 9 > Last line read: > '1 1' > Found a second defaults directive. > > my command line like this- [n...@localhost dmpc1tap]$ grompp -f em.mdp -p > dmpc.top -c dmpc-solvated.pdb -o dmpc-em.tpr > If anyone know about this please help me in solving this problem . > > its very useful for me. > > thank you very much in advance. > > Nitu Sharma > School Of life sciences > Jawaherlal Nehru University > New Delhi, India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090330/cc706c66/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Mon, 30 Mar 2009 11:36:53 +0530 > From: Pawan Kumar <pawan.chin...@gmail.com> > Subject: Re: [gmx-users] grompp error in running simulation of lipid > bilayer > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <143b0c640903292306y6d89c0adm96a27c87cd474...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Greetings from Pawan. > Edit your lipid.itp file. > Comment or remove the lines : > [default] > 1 1 > > Then grompp will work.. > > Regards, > Pawan > > 2009/3/30 nitu sharma <sharmanit...@gmail.com> > > > Dear all , > > > > > > I am trying to do simulation of DMPC lipid > > bilayer for this I have made topology file with the help of teleman > > website by downloading two file -lipid.itp &dmpc.itp . But when I run > the > > grompp for energy minimisation I am getting error like this - > > > > Program grompp, VERSION 4.0.3 > > Source code file: topio.c, line: 430 > > > > Fatal error: > > Syntax error - File lipid.itp, line 9 > > Last line read: > > '1 1' > > Found a second defaults directive. > > > > my command line like this- [n...@localhost dmpc1tap]$ grompp -f em.mdp > -p > > dmpc.top -c dmpc-solvated.pdb -o dmpc-em.tpr > > If anyone know about this please help me in solving this problem . > > > > its very useful for me. > > > > thank you very much in advance. > > > > Nitu Sharma > > School Of life sciences > > Jawaherlal Nehru University > > New Delhi, India > > > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090330/4865e850/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 59, Issue 181 > ****************************************** > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
tip3p.itp
Description: Binary data
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