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 Sun Mar 12 2017 - 21:30:03 PDT
