Hi Alice,
I think the OH bond was missing in your mol2 file for the OH- group, causing O and H were not bonded.
The way to generate the OH- group could be:
(1) Add hydrogen to the oxygen atom as doing in the MCPB.py tutorial: “tleap -s -f wat_tleap.in > wat_tleap.out”, and then delete one of the hydrogen atoms in the PDB file.
(2) Named the PDB file as MOH.pdb, and inside the PDB file rename the residue to something like “MOH” (you can do these things manually by editing the file) to differentiate it from the normal water (which uses “WAT” or “HOH” as its oxygen name)
(3) Use antechamber to generate a MOH.mol2 file by doing:
antechamber -fi pdb -fo mol2 -i MOH.pdb -o MOH.mol2 -at amber -c bcc -pf y -nc -1 -rn MOH
It will gives you a MOH.mol2 file which has OH- group in it.
If you are new to AMBER, I strongly suggest you to read the LEaP tutorial: http://ambermd.org/tutorials/pengfei/ <http://ambermd.org/tutorials/pengfei/> to understand the logics behind it, which could be helpful for your AMBER modeling.
Kind regards,
Pengfei
> On Mar 12, 2017, at 11:25 PM, Alice Zeng <lxzeng.connect.hku.hk> wrote:
>
> Hi,
>
> I want to use MCPB.py to generate zinc Amber force field, there is a hydroxide ion in the Metal centre. How can I deal with the OH and generate the frcmod file for OH?
>
> In the MCPB.py tutorial, I only find the command for water.
> tleap -s -f wat_tleap.in > wat_tleap.out
> antechamber -fi pdb -fo mol2 -i WAT_H.pdb -o WAT.mol2 -at amber -c bcc -pf y
>
> I tried to generate the OH_H.pdb by pymol and used this command to generate the frcmod file.
> antechamber -fi pdb -fo mol2 -i WAT_H.pdb -o WAT.mol2 -at amber -c bcc -pf y -nc -1
>
> Is this right? Cause I met problems when performing the energy minimization process. The hydrogen atom of OH moved away from the oxygen atom of OH, so sander said coordinate resetting (SHAKE) cannot be accomplished, deviation is too large. I think there must be some problems when I used the MCPB.py to generate the parameters of the model.
>
> Best,
>
> Alice
>
> --
> Lingxiao Zeng
> PhD candidate
> School of Biomedical Sciences
> The University of Hong Kong
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Received on Tue Mar 14 2017 - 14:30:02 PDT
