----- 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. > 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
