[gmx-users] specbond .dat connection

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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