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

[Justin Lemkul]

On 4/4/14, 8:47 AM, Ahmet yıldırım wrote:
> Hi,
>
> The bond types are set properly in ffbonded.itp. But I get the following
> errors after grompp command. How can I fix it?
> 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
>
> protein_Ion_chain_A2.itp:
> [ moleculetype ]
> ; Name            nrexcl
> Ion_chain_A2        3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
> ; residue 262 ZN  rtp ZN   q +2.0
>       1         Zn    262     ZN     ZN      1          2       65.4   ;
> qtot 2

If I'm remembering your model right, the Zn-HOH complex doesn't bear a +2 charge 
on Zn.  Is this what you actually want?

> ; residue 1001 OWZ rtp OWZ  q +0.1
>       2         OZ   1001    OWZ     OZ      2    -0.8824         16   ;
> qtot 1.118
>       3         HZ   1001    OWZ    HZ1      2     0.5001      1.008   ;
> qtot 1.618
>       4         HZ   1001    OWZ    HZ2      2     0.5001      1.008   ;
> qtot 2.118
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>      2     3     1
>      2     4     1
>

Apparently whatever ffbonded.itp file that is being read doesn't have these 
parameters.  Unfortunately, there's not enough information to say why.  If OZ-HZ 
parameters were there, there would be no reason they wouldn't be read.

-Justin

> [ angles ]
> ;  ai    aj    ak funct            c0            c1
> c2            c3
>      3     2     4     1
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Ion_chain_A2.itp"
> #endif
>
>
>
>
>
> 2014-04-04 0:32 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 4/3/14, 2:58 PM, Gmail2 wrote:
>>
>>> Dear Justin,
>>>
>>> Zn bound to three Histidine atoms and a water in carbonic anhydrase. This
>>> water bound to Zn has different parameters than solvent water. That
>>> parameters is present in literature. How should I set up such a system?
>>>
>>> PS: I will use 'pdb2gmx' with -vsite hydrogens.
>>>
>>>
>> If you need virtual sites, then you need to figure out how to properly
>> build a virtual site database entry for that particular type of molecule.
>>   That's entirely separate from any of the force field parameters you've
>> shown before, but realize that doing so negates most of the Zn-HOH bonded
>> parameters you posted.
>>
>> -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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>
>
>

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

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

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