Looks like you may have added the bond accidentally? Amber would not add
a bond on its own unless it was in a residue template or if (remote
chance) you had an S ending a chain without a TER in pdb followed by the
ion:
<residue>
ATOM ..S
TER
ATOM ..Zn
The TER tells leap that the molecule chain is complete.
In any case, you could try deleting the bond and it may solve your problem.
Bill
On 8/23/2015 8:49 AM, Jorgen Simonsen wrote:
> Hi all,
>
> I am trying to run a short simulation of an enzyme containing a zinc site -
> I am using leaprc.ff14SB
>
>
> with the following parameters for the ions present in the complex:
>
> loadoff ions08.lib
>
> loadamberparams frcmod.ionsjc_tip3p
>
> loadamberparams frcmod.ionslrcm_cm_tip3p
>
> when I build the complex I get the following error which I guess is that it
> tries to add a bond between the zinc ion and a sulfur atom that is
> coordinating it but I am not sure why it adds a covalent bond and also how
> to solve it
>
> Building bond parameters.
>
> Could not find bond parameter for: Zn2+ - S
>
> Building angle parameters.
>
> Could not find angle parameter: Zn2+ - S - CT
>
> Building proper torsion parameters.
>
> Building improper torsion parameters.
>
> total 1270 improper torsions applied
>
> Building H-Bond parameters.
>
>
> Thanks in advance
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 23 2015 - 14:30:06 PDT
