Hi, I would also strongly recommend replicating some existing work on heme with Fe2+, before grappling with unknowns.
Mark On Wed, Feb 8, 2017 at 3:25 PM Justin Lemkul <[email protected]> wrote: > > > On 2/8/17 1:47 AM, Mehreen Jan wrote: > > Hello, anyone plz help Hopefully you all are doing well. I am using FF: > 43a1 > > Spc watermodel version 5.0.7. > > > > I know parameters for Heme are already available and that is for FE2+. I > want > > to perform MD simulation for FE3+. While running simulation I get error : > > Residue "OXY" not found in residue topology database. I checked .rtp > file and > > that does not include topology for OXY. I checked gromacs mailing list > and > > got the answer that modify specbond . dat file . Kindly please brief me > how > > You have two separate problems. A missing residue is not going to be > fixed by > altering specbond.dat. You need to parametrize the residue appropriately > and > then add it to the .rtp file. See > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > > should I modify specbond .dat file so that I could include oxygen > molecule. > > i read manual 5.6.7 Special bonds but i am still not able to connect OXY > > with HEME. This is my oxygen > > > > HETATM 2414 O1 OXY C1543 5.525 80.353 -6.212 1.00 25.38 > > O HETATM 2415 O2 OXY C1543 4.301 80.342 -6.721 1.00 30.35 > > O > > > > specbond .dat fie : any one plz modify it...... > > > > What have you tried based on the advice I gave you previously? Anything > specific that has failed? Is there something unclear in the manual that > can be > improved? If you want free help, you have to be willing to make some > efforts on > your own; no one's going to do your work for you. We have multiple people > posting identical questions (sometimes minutes apart, and people spamming > my > personal inbox incessantly) all asking for the same thing to be done, yet > no > progress seems to be made... > > -Justin > > > 9 CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 CYS > SG 1 HEM FE 2 0.25 CYS2 HEME CYS > SG 1 > > HEM CAB 1 0.18 CYS2 HEME CYS SG 1 > HEM CAC 1 0.18 CYS2 HEME HIS NE2 1 HEM > > FE 1 0.2 HIS1 HEME MET SD 1 HEM > FE 1 0.24 MET HEME CO C 1 > > HEME FE 1 0.19 CO HEME CYM SG 1 CYM > > SG 1 0.2 CYS2 CYS2 CYZ SG 1 ZN1 ZN > > 1 0.23 CYZ ZN1 > > > > Thanks, Mehreen Jan > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (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 [email protected]. > -- 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 [email protected].
