[AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh

From: Sanaa ALAbbad <salabbad79.gmail.com>
Date: Tue, 17 Oct 2017 17:10:44 -0600


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
for each ligand I searched for the library that will represent each atom
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?

Sanaa AlAbbad
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Received on Tue Oct 17 2017 - 16:30:02 PDT
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