Thank you Peyman
On Thu, 24 Jul 2008 Peyman Yamin wrote : >On Thursday 24 July 2008 09:46, minnale wrote: > > Hi users, > > I have generated .gro file of protein by using .xtc file with trjconv > > command after that i used pdb2gmx command for generating topology file > > without any error. when I have inserted this protein into popc bilayer by > > using genbox command i has deleted some of the water and popc molecules, > > these residues i have mentioned in .top file but when i have used grompp > > command its showing that Fatal error: > > Program grompp, VERSION 3.3.1 > > Source code file: grompp.c, line: 448 > > > > Fatal error: > > number of coordinates in coordinate file (2hel_popc7.6.gro, 12882) > > does not match topology (2hel_noH1.top, 12832) > > > > The same system which is protonated state of protein simulating without > > generated .gro file by using trjconv command its running fine, But above > > mentioned system (unprotonated state) showing some fatal error > > > > Couls you pls tell me some suggestion. > > Thanks in advance > > >[ atoms ] section of the topology file lists and enumerates the atoms of your >molecule. this should correspond to that from the .gro file of the molecule. >in [ molecules ] part of the topology the number of the molecules should be >mentioned correctly. > >if you delete things from coordinate file, you should apply the proper change >to the topology as well. > >it seems you have more atoms in your gro than what is expected from the >topology file. might want to find out why :) > >Peyman > > > > >-- >Peyman Yamin >Lehrstuhl fuer Thermische Verfahrenstechnik >Universitaet Erlangen-Nuernberg >Egerlandstr. 3 >91058 Erlangen >Phone: +49(0) - 9131 - 85 27671 >Mailto: [EMAIL PROTECTED]
_______________________________________________ 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
