No, not this one again! Why not search the archives? Or browse the wiki? Or follow a more extensive tutorial on Gromacs: http://nmr.chem.uu.nl/~tsjerk/course/molmod/ ?
Tsjerk 2009/3/30 Halie Shah <[email protected]>: > > Hi, > > I just finished my energy minimization run on GROMACS 4.0.4 for my > ligand/protein combination. I opened the minimized protein pdb and the > original pdb in VMD to visualize, but saw that my minimized protein was > outside the solvent box I had made. How should this be corrected? Below is > what I specified for my commands: > > editconf -bt octahedron -f BR6.pdb -o BR6.pdb -c -d 0.7 > genbox -cp BR6.pdb -cs spc216.gro -o BR6_b4ion.pdb -p BR6.top > > Do I need to increase my -d value, and if so, to what? My protein is 244 > residues..not too big. Also, is spc216 the right water model I should use? > > Thanks much in advance, > Halie Shah > > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
