[gmx-users] part2-adding metal-bonding parameters to a force field

[Justin Lemkul]

On 4/15/14, 6:20 AM, Ahmet yıldırım wrote:
> Hi,
>
> There are two H1D residue in modified pdb file and one H1E residue. ZN atom
> in H1E are bound to OW and ND1 atoms in H1E and NE2 atom in H1D. That is,
> Zinc has four bond.
>
>                NE2(H1D)
>                   ı
> (H1E)ND1-ZN-OW(H1E)
>                   ı
>                NE2(H1D)
>
> specbond.dat:
> Line 1:H1E    ND1    1       H1E      ZN      1       0.2   H1E    H1E
> Line 2:H1E    OW     1       H1E      ZN      1       0.2   H1E    H1E
> Line 3:H1D    NE2    1       H1E       ZN      1       0.2   H1D    H1E
>
> After pdb2gmx:
> Linking H1D-94 NE2-754 and H1E-119 ZN-920...
> Linking H1D-96 NE2-775 and H1E-119 ZN-920...
> Linking H1E-119 ND1-952 and H1E-119 ZN-920...
> Linking H1E-119 OW-921 and H1E-119 ZN-920..
>
> I know the above linkings are correct.
>
> I wonder, should I change as the following the line 3 in specbond.dat
> because there are two H1D residue in structure?
> H1D    NE2     1     H1E        ZN       2       0.2   H1D   H1E
>

No.  In fact, the number of bonds should probably only be set to 1, because Zn 
only forms one bond with each of the ligating residues.  It's not the total 
number of bonds that can be formed (because that would vary based on each 
system), it's how many bonds are formed between any given pair of residues.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================