Hi, editconf -f waters.pdb -o conf.pdb
As for CHARMM, you may select the atoms of interest and incorporate to your topology (see chapter 5 of the manual) Also maybe some script for the conversion exist, try to search. Vitaly > > Hello everyone, > Thanks to Justin Lemkul and Thomas Schlesier for replying to my question > in vol. 65 issues 96 and 98. > I am trying to convert a pdb file to a gro file using pdb2gmx -f > waters.pdb -o waters.gro and I get the message: > > Select the Force Field: > 0: GROMOS96 43a1 force field > 1: GROMOS96 43a2 force field (improved alkane dihedrals) > 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > 6: [DEPRECATED] Gromacs force field (see manual) > 7: [DEPRECATED] Gromacs force field with hydrogens for NMR > 8: Encad all-atom force field, using scaled-down vacuum charges > 9: Encad all-atom force field, using full solvent charges > > I don't want to use any of these force fields. I want to use the charmm27 > one. How do I select that? Do I need to modify the code? If so, where do I > find it? > Also, I read in a Spidertoxin tutorial that editconf can be used to > convert a .pdb file to a .gro file. I tried this but error message says: "No > velocities found." I know that pdb files generally do not have velocities > and these velocities can be generated by setting genvel=yes in the mdp file. > How can a .pdb file contain initial velocities? > _______________________________________________ gmx-users mailing list [email protected] http://lists.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
