[gmx-users] Re: Water models for amber03 (Justin A. Lemkul)
Alan
alanwilter at gmail.com
Mon Mar 30 10:00:55 CEST 2009
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 <sharmanitu35 at gmail.com>
> Subject: [gmx-users] grompp error in running simulation of lipid
> bilayer
> To: gmx-users at gromacs.org
> Message-ID:
> <5fe39aa90903292301vea30bb9kdb79cebc01b98e11 at 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- [nitu at 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
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> ------------------------------
>
> Message: 7
> Date: Mon, 30 Mar 2009 11:36:53 +0530
> From: Pawan Kumar <pawan.chinari at gmail.com>
> Subject: Re: [gmx-users] grompp error in running simulation of lipid
> bilayer
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <143b0c640903292306y6d89c0adm96a27c87cd47442e at 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 <sharmanitu35 at 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- [nitu at 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
> >
> >
> >
> >
> > _______________________________________________
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> End of gmx-users Digest, Vol 59, Issue 181
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--
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<<
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