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 <bapti...@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" <jalem...@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 <jalem...@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 >>>>> >>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>> http://mackerell.umaryland.edu/~jalemkul >>>>> >>>>> ================================================== >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at http://www.gromacs.org/ >>>>> Support/Mailing_Lists/GMX-Users_List before posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> >>>>> >>>> >>>> -- >>> ================================================== >>> >>> 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 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >>> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- > 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: bapti...@itqb.unl.pt > fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista > -------------------------------------------------------------------------- > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.