[gmx-users] vdw radii in g_sas

[Antonio Baptista]

You can indeed compute ff-dependent atomic radii from nonbonded 
parameters, which might be sometimes convenient (e.g., when trying to 
optimize a particular methodology). Some ways to do that are discussed in 
section 2.5 of http://dx.doi.org/10.1021/jp052259f.

However, note that the surfaces, volumes, etc computed by tools like g_sas 
are physically vague properties. They are based on a geometrically 
well-defined but somewhat arbitrary algorithm (Lee-Richards, Connolly, 
etc), an idealized spherical solvent probe, and a vaguely defined set of 
"atomic radii" -- even if you use experimentally-derived "van der Waals 
radii", their relation with the data (and thus their physical meaning) is 
neither straightforward nor unique.

Since the properties that g_sas computes are physically vague, the 
important thing is to not depart too much from the usual methodology and 
allow others to reproduce your results. So, unless you are trying to do 
something unusual (as in the paper cited above), use the default GROMACS 
values and cite the version (which has a unique vdwradii.dat), or use 
instead a familiar set of radii (e.g., Bondi) and cite the corresponding 
paper.

Cheers,
Antonio

On Fri, 9 May 2014, Tsjerk Wassenaar wrote:

> 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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--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619         email: baptista at itqb.unl.pt
fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~baptista
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