On 6/20/14, 10:12 AM, mirko busato wrote:
Thank you, I understood, you are right, in the .rtp file there are not neutral form for the termini. What can I do to have a neutral arginine, to have at least a total charge of 0? Because In my case I am forced to choose ARG protonated else I get the error. Fatal error "In the chosen force field there is no residue type for 'ARGN' as an ending terminus"
Use a force field that has parameters for a neutral form. I'm sure someone has produced parameters for such a species, but they're not included in Amber99SB by default. If parameters are out there, add them (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field), otherwise use a different force field.
-Justin
Thank you very much, Mirko On Thursday, June 19, 2014 3:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 6/19/14, 8:59 AM, mirko busato wrote: > Thank you very much for your quick reply, > > My peptide is only composed of amino acids, and it has a total charge of 0. > My termini are NH2 and COOH (so the termini are not ionized). My force field is > amber99sb. > I tried to change for all atoms of my first residue (ASN) the ASN residue with > the NASN residue name. In the first residue (ASN) there are the 3 atoms of N > terminal . In the same way for ARG (the last residue ) with CARG. > Look at the force field .rtp file - you will see that the Amber termini are predefined and they are always charged. That is an unfortunate limitation to the current implementation. I suspect someone must have produced neutral forms of the termini, but you'll have to add them yourself if you want to do such a simulation with this force field. > With -inter option in the pdb2gmx command, > If I select Not protonated ARG (charge 0) and the other residues with charge 0, > at the end the command says: > Fatal error > "In the chosen force field there is no residue type for 'ARGN' as an ending > terminus" > This option chooses the side chain protonation state, not the terminus. > if I select protonated ARG (charge 1) and the other residues with charge 0, I > obtain charge 1 (it is obvious) but my NH2 termini is changed to NH3 and my > COOH in COO. (The command works but in my case the result is wrong because the > total charge has to be 0 with NH2 and COOH termini, not ionized). > > I don't understand if in my case I have to change ASN to NASN only for the 3 > atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C > terminal ( C,O2,O1,H) > > or change for all atoms of the first residue (ASN), ASN with NASN, and change > all atoms of the last residue (ARG) , ARG with CARG.( that I done and described > before).. > If this is the right way, I don't know how to obtain the right result for my > peptide. > As stated above, you'll have to modify the force field to add appropriate parameters or otherwise use a different force field that actually allows you to choose terminus protonation state. -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 <mailto:jalem...@outerbanks.umaryland.edu> | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ==================================================
-- ================================================== 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.
