Re: [gmx-users] vdw radii in g_sas
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.ptwrote: 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
[gmx-users] vdw radii in g_sas
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. Thanks, -- 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.
Re: [gmx-users] vdw radii in g_sas
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.
Re: [gmx-users] vdw radii in g_sas
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.
Re: [gmx-users] vdw radii in g_sas
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.
