I'm trying to compare the hydrophobic surface generated from my trajectory with g_sas to a range of random coil .pdb files with my protein sequence, but I can't figure out how to make the structure+mass input that is required for g_sas from my pdb files i.e. in the manual "Structure+mass(db): tpr tpb tpa gro g96 pdb" Just using the pdb file itself results in it not being able to define which residues are hydrophobic and it doesn't work. I want the two calculations to be as comparable as possible.
Thanks for any help people can give. Erin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-sas-on-pdb-files-tp5009248.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
