[gmx-users] vdw radii in g_sas

[Justin Lemkul]

On 5/9/14, 3:35 PM, rajat desikan wrote:
> 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?
>

Google knows.

-Justin

> 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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>
>

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

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

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