[gmx-users] g_sas; could not find a Van der Waals radius

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 17 15:30:11 CET 2012

afsaneh maleki wrote:
> 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?

Well, you're trying to calculate SASA and g_sas doesn't know how to incorporate 
P atoms into that calculation, so my guess is that yes, this warning is quite 

> 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?

The vdwradii.dat file is the correct place for this information.  The data 
presently there lack references, and there has been a lot of discussion in the 
past on whether or not these values are reliable.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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