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

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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
; 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

[ 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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