Quoting [EMAIL PROTECTED]: > Thanks for the suggestions but just to make my problem more clear.... > > The "genion" command that I used is: > > /opt/gromacs/bin/genion_mpi -s em.tpr -o ce_myoII_frag0_neu.gro -g > genion.log -np 2 -pname Na+ > > And the topology file is: > > Before adding ions: > > [ molecules ] > ; Compound #mols > Protein 1 > SOL 2818598 > > After adding ions: (modified) > > [ molecules ] > ; Compound #mols > Protein 1 > SOL 2818600 > NA+ 2
There's the problem. Think about it - you just replaced two water molecules with two Na+, but instead you've added two more water molecules, on top of adding your ions. -Justin > > > > > Dear All > > When I run the command "genion" specifying the number n type of chrges to > be added, it works fine. I also have made changes in my topology file. But > somwhow when I run the "grompp" after that it gives me the following > error... > > processing topology... > Generated 380 of the 1326 non-bonded parameter combinations > Excluding 3 bonded neighbours for Protein 1 > Excluding 2 bonded neighbours for SOL 2818600 > Excluding 1 bonded neighbours for Na+ 2 > NOTE: > System has non-zero total charge: -2.399999e+01 > > processing coordinates... > ------------------------------------------------------- > Program grompp_mpi, VERSION 3.3.1 > Source code file: grompp.c, line: 448 > > Fatal error: > number of coordinates in coordinate file (ce_myoII_frag0_neu.gro, 8461523) > does not match topology (ce_myoII_frag0.top, 8461535) > ------------------------------------------------------- > > I tried adding 2 and 3 ions to the system. But it seems to give the same > error. Could someone help? > > Thanks > Namitha Mohandas > > > > _______________________________________________ > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
