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

[Justin Lemkul]

On 4/4/14, 1:46 PM, Ahmet yıldırım wrote:
> Dear Justin,
>
> These parameters are present in literature. I think these bonds/parameters
> are correctly generated. You said "The previous topology output suggests
> not, because ZN is not renamed to ZNW".  I do not know what to do.
>

Probably because the distance you have set in specbond.dat is incorrect.  I'll 
ask again - are the His-Zn bonds correctly generated?  If not, that's your 
problem.  If they are, we'll have to do more digging.  You can avoid the whole 
Zn-renaming and charge issue if you do as I suggested before and create a 
residue that contains Zn(HOH), not just ZN and then a separate residue for the 
water bound to it.  Treat it as its own entity.

> I added the OZ-HZ bond in ffbonded.itp. Unfortunately I get the same errors:
>
> ERROR 1 [file protein_Ion_chain_A2.itp, line 33]:
>    No default Bond types
> ERROR 2 [file protein_Ion_chain_A2.itp, line 34]:
>    No default Bond types
>
> ffbonded.itp:
>    Zn NA         1    0.20500   16744.0 ;modified
>    Zn NB         1    0.20500   16744.0 ;modified
>    Zn OZ         1    0.23000   16744.0 ;modified
>    OZ HZ         1    0.09572   221682.2 ;modified
>

Are you making these corrections in the right place?  Does your .top call your 
modified force field?  Are you modifying files in $GMXLIB or in the working 
directory?

-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

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