> ----- Original Message ----- > From: Jens Pohl <[EMAIL PROTECTED]> > Date: Thursday, February 14, 2008 12:25 am > Subject: [gmx-users] Strange output with Genbox > To: [email protected] > > > 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... > > It's not easy to be sure exactly what you're describing here, but I think you > mean that genbox is placing waters inside the expected vdW surface of your > protein. If so, then check out "genbox -h" for how GROMACS works out this > surface. Otherwise, please consider posting a picture to a website somewhere.
The water is placed in between the chain. When I have a look at the sequence there is water followed by AA followed by water. I've done a similar simulation before and there the sequence was Protein first and the the water residues. > > 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 > > Mark > _______________________________________________ > 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 > Jens _______________________________________________________________________ Jetzt neu! Schützen Sie Ihren PC mit McAfee und WEB.DE. 30 Tage kostenlos testen. http://www.pc-sicherheit.web.de/startseite/?mc=022220 _______________________________________________ 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
