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 <gmx-users@gromacs.org> 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 <gmx-users@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 >> >> >> -- _______________________________________________________ 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 gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
files.rar
Description: Binary data
_______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php