Hello,
Alternatively, you could use "ante-mmpbsa.py" to get the necessary files.
Best Regards
Elvis A F Martis
Molecular Simulations Group,
Department of Pharmaceutical Chemistry,
Bombay College of Pharmacy,
Kalina, Santacruz [E],
Mumbai 400098,
INDIA.
Institute Web-address: www.bcp.edu.in<http://www.bcp.edu.in>
Research Group Web-address: www.profeccoutinho.net.in<http://www.profeccoutinho.net.in>
Personal Web-address: www.elvismartis.in
________________________________
From: Qinghua Liao <scorpio.liao.gmail.com>
Sent: 31 December 2018 20:42
To: amber.ambermd.org
Subject: Re: [AMBER] Obtaining necessary *.top for MMPBSA.py
Hello,
You can either use tleap to generate the topology files or use parmed to
do that.
With tleap, you would need to run three times, for the complex, the
receptor and the ligand, respectively.
While with parmed, you would need to strip water and ions for the
complex, strip water, ions and the ligand for receptor,
and strip water, ions and the receptor for the ligand.
All the best,
Qinghua
On 12/31/18 3:08 PM, Sundar wrote:
> How to generate com.top, rec.top, lig.top and solvated_com.top files from
> an existing solvated_com.prm7 and solvated_com.mdcrd to be used for MM/PBSA
> calculation with MMPBSA.py ?
>
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Received on Mon Dec 31 2018 - 21:30:03 PST
