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 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