Re: [AMBER] Stability MMPBSA

From: Parker de Waal <>
Date: Tue, 31 Mar 2015 02:47:00 +0000

I found the answer to my question ‹ I noticed that the wt PDB was
including the POPC atoms while the mutant was not.

To fix this I appended the POPC atoms in

strip_mask = ':WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+,OL,PC,PAı

However Iım still skeptical is this is an appropriate method for protein
stability calculations for membrane proteins.

If anyone could comment on this I would greatly appreciate it.

On 3/30/15, 9:44 PM, "Parker de Waal" <> wrote:

>Hi Everyone,
>Iım trying to perform alanine scanning on a GPCR in an explicit POPC
>membrane to assess energy contribution to protein stability.
>Unfortunately, each time I try to run the program the following
>error occurs:
>For input I am using:
>-sp 033015.prmtop (solvent complex in membrane)
>-cp proteinOnly.prmtop (protein only)
>-y (traj)
>-mc 40.prmtop (residue 40 mutated to ala)
>Iıve upload my input files to dropbox and they can be found here:
>Any insight would be truly appreciated.
>AMBER mailing list

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Received on Mon Mar 30 2015 - 20:00:02 PDT
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