[AMBER] MM-PBSA Alanine scanning issue

From: YOGESH NARKHEDE <yogesh.pi.niper.gmail.com>
Date: Fri, 9 Aug 2019 10:44:00 -0700

Hello everybody,
I had a query regarding alanine scanning of a complex which I asked a few
days back. Since, I have had no replies, I am reposting it hoping to get a
discussion or an answer.

I am using MMPBSA to run an alanine scan on a complex. The focus of my
experiment is not on computing the binding free energy of a ligand to the
protein. However, I am interested in the alanine scanning results for the
complex (protein only).

I followed the tutorial for the RAS-RAF system (section 3.3) to the letter
and got consistent results. In this section, the command for MM-PBSA is:

AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp ras-raf_solvated.prmtop -cp
rasraf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd -mc
rasraf_mutant.prmtop -mr ras_mutant.prmtop

I do have the topology files corresponding to the following flags:
-sp (solvated complex)
-cp (gas phase complex)
-rp (gas phase receptor)
-mc (mutated complex)
-mr(mutated receptor)

However, since I am interested in the effect of mutations on the deltaG of
solvation , the flags "-rp ras.prmtop -lp raf.prmtop” become somehow
irrelevant in my case. It is difficult for me to figure out how to proceed
further in this case.

I appreciate any help/discussion in this regard.


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Received on Fri Aug 09 2019 - 11:00:03 PDT
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