[gmx-users] How to connect ligating residues ??

[Justin Lemkul]

On 2/6/17 12:13 AM, Mehreen Jan wrote:
> Hello,
>          Hope so you are doing well. Thanks a lot for your kind response.
> Version : 5.0.7
> FF: 43a1 Spc water model.
>
> Your Suggestion:
> "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."
>
> This oxygen molecule is attached as a ligand to heme.
> 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
>
> Now my question is how connections to ligating residues should be recognized via existing entries in specbond.dat.
>
> 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
>
> Waiting for your kind response. I shall be very thankful to you.

Please read manual section 5.7.7.

-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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