[gmx-users] vdw radii in g_sas

Mon May 12 09:05:37 CEST 2014

Hi All,
I am extremely sorry for the blooper in the above mail. I meant to write
g_mdmat, but it came out as g_sas!  Please give me any heuristic
suggestions for choosing the truncation distance, if any.

Thanks,

On Sat, May 10, 2014 at 11:47 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> 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
>

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