Hi Sanaa,
You can use the “add_bonded_pairs” variable to solve the problem:
Please see Page 296-297 in
http://ambermd.org/doc12/Amber17.pdf <
http://ambermd.org/doc12/Amber17.pdf>.
Note that there is a typo in the example of the manual (in the top of Page 297), which should be:
"add_bonded_pairs 1001-1320 1001-1380”
In which the bonded pairs should be connected by the dash symbol.
Kind regards,
Pengfei
> On Oct 17, 2017, at 6:10 PM, Sanaa ALAbbad <salabbad79.gmail.com> wrote:
>
> Hi AMBERs,
>
> I am trying to create bonds between Ru and the ligands.(bipyridine, two
> PPh3, CO, and hydride). when I followed the Os example of using MCPB, it is
> only identified the Ru-bipyridine bonds.
>
> So I tried to use genMetalFF.sh. following the steps in the link
> http://ambermd.org/tutorials/advanced/tutorial20/mcpb.htm
> for each ligand I searched for the library that will represent each atom
> type.
> I will give the phosphorous as example of what I have done:
>
> 1- in the pdb file there are 2 atoms
> ATOM 3 P PPA A 3 -0.992 -0.027 -2.444 0.00
> 0.00 P
> ATOM 4 P PPA A 4 -0.995 -0.021 2.440 0.00
> 0.00 P
>
> 2- in the script I edited it as
>
>> copyStdResidue terminal/PPA NAME/PP1
>> copyStdResidue terminal/PPA NAME/PP2
> #####
>> copyAtomType parm_gaff/p5 NAME/P1
>> copyAtomType parm_gaff/p5 NAME/P2
> ####
>> setAtomType NAME/PP1/...P NAME/P1
>> setAtomType NAME/PP2/...P NAME/P2
> ####
>
> the error:
> Incorrect use of setAtomType: Can't find stdAtom: P
>
> Any idea?
>
> Thank
> Sanaa AlAbbad
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Received on Wed Oct 18 2017 - 09:30:02 PDT
