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

[Justin A. Lemkul]

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 
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?
> 

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================