[gmx-users] problem with MD

[Dastmalchi]

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:

...
...
...
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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