[gmx-users] vdw radii in g_sas

Sat May 10 20:17:50 CEST 2014

Thank you Justin, Tsjerk and Antonio for your detailed answers.

g_sas computes uses the truncation distance for residue contacts by
considering the minimum distance between residues. However, the papers I
referred to has a Calpha-Calpha or Cbeta-Cbeta cutoff of 10-12 angstrom
(default g_sas truncation criteria is 1.5 nm). Can anybody give heuristic
suggestions about the truncation distance value?

Thank you all for your time.

On Sat, May 10, 2014 at 7:15 AM, Antonio Baptista <baptista at itqb.unl.pt>wrote:

> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
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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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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore