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

[sebastien santini]

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
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>   


-- 
_______________________________________________________

 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
_______________________________________________________