Hi Andres, in total you have 10475 (198+10277) SOL molecules, so you can condense the two SOL lines into one. Suppose you add 20 NA+ and 20 CL-, you subtract 40 SOL molecules from the system and add 40 ions in total. So you write:
[ molecules ] ; Compound #mols Protein_A 1 SOL 10435 NA+ 20 CL- 20 There are now 40 SOL molecules less (10475-30=10435) and the ions are added. Don't forget to add an #include "ions.itp" under "Include generic topology for ions" Marcus Andres Rojas Guerrero wrote: > Hi, I'm newbie in Gromacs and MD, I'm reading the Tsjerk excellent > tutorial. In the part of Addition of Ions, Tsjerk said that we need to > edit the topology file and the decrease the number of solvent molecules, > and add a line specifying the number Na+ and Cl-. How can I do this? > Let me explain, in the topology file I have: > > [ molecules ] > 10565 ; Compound #mols > 10566 Protein_A 1 > 10567 SOL 198 > 10568 SOL 10277 > > What number I need to change? and what it's the fomat to add the ions > Na+ and Cl- to topology file? > > Thank you very much. > > Andres. > _______________________________________________ > 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 thewww > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Marcus Kubitzki Max Planck Institute for Biophysical Chemistry Computational Biomolecular Dynamics Group Am Fassberg 11 D-37077 Göttingen Germany phone: ++49-551-2012312 fax: ++49-551-2012302 Email: mkubitz[at]gwdg.de www: http://www.mpibpc.mpg.de/groups/de_groot/ _______________________________________________ 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
