[gmx-users] vdw radii in g_sas

[rajat desikan]

Thanks Justin. I am curious about the value for a phosphorus atom (protein
in phospholipid bilayer; g_sas issues a warning). Do you know any reference
for experimental values?

On Friday, May 9, 2014, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/9/14, 12:23 PM, rajat desikan wrote:
>
>> Hi All,
>> In the local copy of vdwradii.dat for g_sas calculations, the vdw radii
>> are
>> very approximate.
>>
>> Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm
>> => vdwradius=0.185 nm
>>
>> Is it prudent to replace the values in the local vdwradii.dat with the
>> vdwradii derived from ffnonbonded values? I would love to hear your
>> thoughts/suggestions.
>>
>>
> No.  The value of sigma will not give you the van der Waals radius of an
> atom. For each force field, the value is different, and it is based on
> optimized intermolecular distances.  I don't think there's a clear way to
> turn this into some measure of an atom's size.
>
> If you're concerned that the values in vdwradii.dat are not sufficiently
> accurate, replace them with real experimentally determined values.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore