[gmx-users] specbond .dat connection
jalemkul at vt.edu
Wed Feb 8 15:25:35 CET 2017
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
> 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
> 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...
> 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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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