[AMBER] Alanine scan issue

From: YOGESH NARKHEDE <yogesh.pi.niper.gmail.com>
Date: Tue, 6 Aug 2019 10:59:51 -0700

Dear all,

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, I do not have any ligand bound to the system, which makes the "-rp
ras.prmtop -lp raf.prmtop” commands irrelevant. 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 Tue Aug 06 2019 - 11:30:02 PDT
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