Re: [AMBER] MM-PBSA Alanine scanning issue

From: Elvis Martis <>
Date: Sat, 10 Aug 2019 09:53:18 +0530

Best Regards

On Fri, 9 Aug 2019 at 23:16, YOGESH NARKHEDE <>

> 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).
> >> Since you are not including ligand prmtop for the calculations,
> will only calculate protein stabiliy.

> 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/ -O -i -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)

> > I am not very sure this will work, but try just try using -sp,-cp and
> -mc. This should give you a ddG for protein stability upon mutation.
> 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.
> > In this case you, do not provide -lp and -rp, as you say they are
> irrelevant in your case.

> I appreciate any help/discussion in this regard.
> Thanks,
> Yogesh
> --
> Yogesh
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Received on Fri Aug 09 2019 - 21:30:02 PDT
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