[AMBER] suggestion for generation of prmtop and inpcrd file at different pH

From: Vikram Dalal <vikram.dalal.37.gmail.com>
Date: Thu, 4 Jun 2020 02:34:52 +0530

Hello Everyone,

I have to run the molecular simulation of a protein-ligand complex having
cofactors and metals at different pH i.e. neutral, acidic and basic.

I am aware of H++ server for processing files at different pH. But this
server can maximum consider 1 ligand with protein.

I have generated the pdb for protein at specific pH like neutral or basic.
Then generated the promtop and inpcrd by providing the h++ generated pdb
for protein along with mol2 and frcmod of cofactors and metals in TLeap.
I have successfully run the molecular simulation using these files.

I would like to know whether the strategy used by me is right or not. If it
is wrong, let me know how to proceed with molecular simulation at different
pH for my protein-ligand complex having cofactors and metals.

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Received on Wed Jun 03 2020 - 14:30:02 PDT
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