On 9/9/14 3:51 PM, Agnivo Gosai wrote:
Dear Users I am trying to find the net charge at the physiological pH value for a protein molecule (Thrombin) in my case and am wondering if it is possible to use GROMACS for doing it. I am very new to GROMACS and at present I have been going through the tutorials by Dr. Lemkul. I have seen that the topology file generated by "pdb2gmx" contains the total electron charge value for a molecule. I was wondering if this can be used to get the charge value for Thrombin at physiological pH.
Gromacs will assume canonical protonation states at pH 7 for all residues (unless you reassign them manually, in which case there's really no point in running pdb2gmx because you know the answer). Whether or not this assumption is valid depends on the actual pKa values of the constituent amino acids. There are much more rigorous ways to calculate the net charge of a protein; I'd suggest you look at other servers and methods. There is a huge community of people who do pKa predictions.
-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.
