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,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.
Parker
On 3/30/15, 9:44 PM, "Parker de Waal" <Parker.deWaal.vai.org> 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 MMPBSA.py program the following
>error occurs: https://gist.github.com/anonymous/5ce740cb6d64953b72a9
>
>For input I am using:
>-sp 033015.prmtop (solvent complex in membrane)
>-cp proteinOnly.prmtop (protein only)
>-y traj.nc (traj)
>-mc 40.prmtop (residue 40 mutated to ala)
>
>Iıve upload my input files to dropbox and they can be found here:
>https://www.dropbox.com/s/wpxygrszfdzasw9/mmpbsa.tar.gz?dl=0
>
>Any insight would be truly appreciated.
>
>Best,
>Parker
>
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Received on Mon Mar 30 2015 - 20:00:02 PDT
