[gmx-users] how to link connections to ligating residues

[Justin Lemkul]

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
> END
>
> The specbond.dat file contains the following:
> 8
> 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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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