Hi, I have a system that is contained of Protein-DOPC-SOL-Ions. I want to calculate residue SAS of protein.The calculation group consists of all the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14 ion),and then protein for output. Force files used for protein and DOPC are ffg53a6 and Berger respectively.
When I use g_sas I obtain the following message: WARNING: could not find a Van der Waals radius for 125 atoms. I have two questions. Q1- This warning is important? Q2-Is the valid source to get data for Van der Waals radius of phosphorous atom to insert in the vdwradii.dat file? I think this warning is about phosphorous atoms of DOPC. what is Van der Waals radius of phosphorous atoms that will be right for this goal? Thanks very much in advance, afsaneh -- 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
