[gmx-users] problem with position-restrained dynamics of a charged system

[OZGE ENGIN]

Yes, Sebastien! It ends as you wrote. So, it contains info about the numbers of atoms, and it worked for the previous step. I could not understand the problem :(



-----Original Message-----
From: sebastien santini <santini.s at fsagx.ac.be>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Tue, 22 May 2007 14:27:18 +0100
Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system

It seems your topology does not contain any information about number of 
atoms etc ...

Does your file end with lines like this (for example):

...
[ molecules ]
; Compound   #mol
Protein                 1
NA+                  12
SOL              1589



OZGE ENGIN a écrit :
> Hi all,
>
> I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step:
>
> Fatal error:
> number of coordinates in coordinate file (lysine_b4pr.gro, 767)
>              does not match topology (lysine.top, 0)
>
> I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem?
>
> Thanks in advance!
>
> Ozge Engin
>
>
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-- 
_______________________________________________________

 Sébastien SANTINI, PhD
 
 http://sebastien.santini.free.fr
 
 CBMN, Faculté Universitaire des Sciences Agronomiques  
 Passage des déportés, 2  
 B-5030 Gembloux, BELGIQUE

 GSM: 00 32 (0)4 98 59 53 65
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