On Mon, Mar 30, 2015 at 10:47 PM, Parker de Waal <Parker.deWaal.vai.org>
wrote:
> 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 input_parser.py:
>
> 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.
>
P
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 MMPBSA.py 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
MMPBSA.py parsers will handle the output correctly).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 31 2015 - 05:30:03 PDT
