Re: [AMBER] Stability MMPBSA

From: Jason Swails <>
Date: Tue, 31 Mar 2015 08:05:52 -0400

On Mon, Mar 30, 2015 at 10:47 PM, Parker de Waal <>

> 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,PA¹

​Why not just set strip_mask in the input file instead?

> ​​
> However I¹m still skeptical is this is an appropriate method for protein
> ​​
> stability calculations for membrane proteins.

​robably not, although it depends on what thermodynamic cycle you're trying
to solve. Note, PBSA supports membrane simulations (which may be what you
want), but I don't know if really supports those options (for
sure, you would need to use -create-mdins and -use-mdins after modifying
the input files to run a membrane simulation, but I'm not positive that the parsers will handle the output correctly).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Mar 31 2015 - 05:30:03 PDT
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