[gmx-users] vdw radii in g_sas

[Tsjerk Wassenaar]

Do mind that the radius for P in PO4 is different from that for P alone.

Cheers,

Tsjerk
On May 9, 2014 10:53 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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