[gmx-users] g_sas; could not find a Van der Waals radius
maleki.afsaneh at gmail.com
Fri Mar 16 23:50:44 CET 2012
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,
More information about the gromacs.org_gmx-users