[gmx-users] problem with MD

[Dastmalchi]

Hi David,
Thanks fror that, but I have compleated the GROMACS Tutorial for Drug-Enzyme
Complex (by John E Kerrigan, http:/www2.umdnj.edu/~kerrigje) on the same
machine with no problem.
Siavoush


> 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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