Your topology file contains
SOL 2490
and your coordinate file only 249 water molecules
change 2490 to 249 in the top file and see what happens.
OZGE ENGIN a écrit :
Thank you very much for your attention :) I attached the needed gro and top files.
-----Original Message-----
From: sebastien santini <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Date: Tue, 22 May 2007 14:52:13 +0100
Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged
system
Maybe you have forget to include something (I don't know exactly what)
...
is it possible to post your top and gro files (attached and zipped) ?
it will be easier to find what happened :P .
OZGE ENGIN a écrit :
Yes, Sebastien! It ends as you wrote. So, it contains info about the number of atoms, and it worked for the previous step. I could not understand the problem :(
-----Original Message-----
From: sebastien santini <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
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
_______________________________________________________
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
