Hello! I try to simulate a modified protein in a water-box. When I use genbox and have a look on the output-file then the water molecules are located in between the AA-sequence which results in an "exploding" molecule during the mdrun. I've done it several times from the very beginning, always getting a similar result (distribution of water in the AA sequence varied a bit).
Input-sequence (AA): MGVLAI... Output after genbox: OMOGOOVOLOAOIOO... Commands used (copied from .bash_history): pdb2gmx -f 165_in.pdb -p 165 -o 165 -n 165 -i 165 -q 165_out.pdb (used ffG53a6) editconf -f 165 -o CbzE_ec.pdb -bt cubic -vol -d 1.0 genbox -cp 165_ec.pdb -cs ../Water.gro -o 165_gb.pdb -p 165_gb Thank you very much in advance for your suggestions to solve the problem Jens _____________________________________________________________________ Unbegrenzter Speicherplatz für Ihr E-Mail Postfach? Jetzt aktivieren! http://www.digitaledienste.web.de/freemail/club/lp/?lp=7 _______________________________________________ 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
