Re: [gmx-users] Using GROMACS to find the net charge on a Protein
Dear Agnivo Regarding your inquiry: there is an online tool to determine the pka value of a protein (of its aminoacids) if you have the pdb file of your protein The program is Propka see it at internet ,( See the paper Very Fast Empirical Prediction and Rationalization of Protein pKa Valuesde Hui Li, Andrew D. Robertson and Jan H. Jensen, in PROTEINS: Structure, Function, and Bioinformatics 61:704 ?721 (2005)) You should look if the pH, which you need, is o that the corresponding value of pka and then you should determine the protonation state of the protein . The pdb2gmx program has the option of being interactive with respect to those aminoacids that have negative or positive charge depending of its pka and the PH ( Glu.Asp, lys, Arg and hys).See that hys at physiological pH has no charge. Best Regards, Chris Agnivo Gosai agnivo2...@gmail.com ha escrito: 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. Thanks Regards Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University -- 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. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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.
[gmx-users] Using GROMACS to find the net charge on a Protein
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. Thanks Regards Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University -- 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] Using GROMACS to find the net charge on a Protein
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.
Re: [gmx-users] Using GROMACS to find the net charge on a Protein
Quick answer is no. In fact, that's really not what (standard) molecular dynamics is for. You need a constant-pH MD method for that. Read this to get a bit more acquainted with the subject (might be overkill for you, because I doubt this is what you want/need): http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Either way, if you really don't need a lot of detail and an approximate protein net charge will do, why not just look at the pKa's of each amino acid and try to work out what the net charge would be for a given pH? It's a quite simple exercise to do with pen and paper and you're never going to be that far off from reality. If the protein is too large, just script it or search the web for a tool to do such. I bet there are a few. P.S. no.1: pdb2gmx knows nothing about pH. It will set the most likely charge for each amino acid at pH 7. It's as accurate as the pen and paper method I suggested. This tool's purpose has little or nothing to do with what you need. P.S. no.2: Have you done your literary research properly? I never worked with thrombin but it doesn't sound very exotic. I bet there are some titration studies of it. Best regards, João Henriques On Tue, Sep 9, 2014 at 9:51 PM, Agnivo Gosai agnivo2...@gmail.com 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. Thanks Regards Agnivo Gosai Graduate Student Mechanical Engineering Iowa State University -- 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.
