[gmx-users] problem with MD

[David van der Spoel]

On Mon, 2003-11-17 at 06:23, Dastmalchi wrote:
> Dear Anton and other GMX users
> 
> As you have suggested I have tried to perform EM and MD with position
> restraints. I have tried so many different situations but so far no luck. A
> few questions came into my mind which may help to find the source of problem
> with my system.
> 1. Is there any limitation on the number of residues?
> 2. Is it possible that itp file that I have for my ligand "mte.itp" be
> problematic? I see the followings messages when I run the grompp on the
> screen:
the problem seems to be that you are using a DOS machine iso Linux/Unix.

You would have to convert your files to dos format or vice versa, or
upgrade to Linux.

> ...
> ...
> ...
> calling bin\cpp...
> In file included from ald_s_m.top:12:
> mte.itp:26: unterminated character constant
> mte.itp:27: unterminated character constant
> mte.itp:28: unterminated character constant
> mte.itp:29: unterminated character constant
> mte.itp:47: unterminated character constant
> mte.itp:48: unterminated character constant
> ...
> ...
> ...
> mte.itp:237: unterminated character constant
> cpp exit code: 33
> Tried to execute: 'bin\cpp -IC:\Gromacs\share\top ald_s_m.top >
> gromppa02664'
> processing topology...
> WARNING 1 [file "mte.itp", line 173]:
> Duplicate atom index (15) in angles
> ...
> ...
> ...
> 
> I think I can see the duplicate in the mte.itp file and can fix it, but
> unterminated character constant?
> 
> By the way, how can I select Protein and Ligand in a system containing
> Protein+Waters for the purpose of energy analysis using g_energy?
> 
> Many thanks for your kind attention in advance.
> 
> Cheers, Siavoush
> 
> ----- Original Message -----
> From: "Anton Feenstra" <feenstra at chem.vu.nl>
> To: <gmx-users at gromacs.org>
> Sent: Monday, November 03, 2003 1:39 PM
> Subject: Re: [gmx-users] problem with MD
> 
> 
> > Dastmalchi wrote:
> >
> > > Dear Anton
> > >
> > >
> > >>Did you first do (in this order): EM and MD with position restraints?
> > >
> > >
> > > Yes, that was the order, but I am not sure about the position restraints
> > > bit. I followed exactly the tutorial.
> > >
> > >
> > >>Where there any problems/errors/warnings/strange things during that?
> > >
> > >
> > > AS the expected files were generated, I didn't really pay close
> attention to
> > > this. However I attach the log file and will appreciate if you could
> kindly
> > > let me there is something wrong with the EM.
> >
> > Hmm, it seems as thouhh the EM was not very effective. Did you use
> constraints?
> > Did you use 'flex_spc'? (sorry, I'm too lazy to chech what the tutorial
> says...)
> > Did you EM your protein and/or ligand first without solvent?
> > My default equilibration setup is:
> > 1) EM protein + ligand in vacuum (include possible crystal waters,
> >        optionally with position restraints on prot+lig(+water) )
> > 2) add water (genbox, do not remove crystal waters)
> > 3) EM prot+lig+water, with posres on prot+lig
> > 4) MD prot+lig+water, with posres on prot+lig
> > 5) 'production MD' (normally without posres).
> >
> >
> > --
> > Groetjes,
> >
> > Anton
> >   _____________ _______________________________________________________
> > |             |                                                       |
> > |  _   _  ___,| K. Anton Feenstra                                     |
> > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> > |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> > | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> > |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> > |             | "If You See Me Getting High, Knock Me Down"           |
> > |             | (Red Hot Chili Peppers)                               |
> > |_____________|_______________________________________________________|
> >
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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