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

sebastien santini santini.s at fsagx.ac.be
Tue May 22 15:27:18 CEST 2007

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
 CBMN, Faculté Universitaire des Sciences Agronomiques  
 Passage des déportés, 2  
 B-5030 Gembloux, BELGIQUE

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