[gmx-users] how to link connections to ligating residues
jalemkul at vt.edu
Tue Feb 7 13:47:01 CET 2017
On 2/7/17 1:04 AM, Shumaila Khan wrote:
> Hello Sir,
> Hopefully you are doing well. As I am new to GROMACS, I am facing problems.
> I read your comments and You suggested someone that "You should not need external servers to generate a heme topology; GROMOS already supports it. It's called HEME and it's in the .rtp file. Connections to
> ligating residues should be recognized via existing entries in specbond.dat."
> I am using
> Version : 5.0.7
> Force Feild : 43a1 Spc water model.
> The ligand attached to heme is oxygen molecule.
> HETATM 1 O1 OXY C1543 5.525 80.353 -6.212 1.00 25.38 O
> HETATM 2 O2 OXY C1543 4.301 80.342 -6.721 1.00 30.35 O
> The specbond.dat file contains the following:
> 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
> Kindly please guide me, how connections to ligating residues should be recognized via existing entries in specbond.dat?
I answered this identical question yesterday. It appears several people are
posting identical questions and perhaps not talking to one another or not
reading other posts outside their own. Please see my other responses and
suggestion regarding appropriate manual sections.
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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