Greetings,
I want to run MMPBSA.py script using 3 different trajectories (complex,
receptor, ligand). The difference between the receptor and the complex
trajectories was that the receptor had an aspartate protonated which was
unprotonated in the complex. This is perfectly fine in reality, but when it
attempted to use MMPBSA.py the program complained. So I modified the
receptor trajectory and topology by removing the extra proton from the ASP
side-chain. However, I still get a residue mismatch error that may be cause
by the modification I introduced. Do you believe this is the case? If yes,
is there any work around to fix it?
Below is my input script:
endframe=1000 -> stop analyzing when endframe is reached
> interval=100 -> analyse every 1000th frame
> keep_files=2 -> 2: Keep all temporary files. Temporary files are only
> deleted if MMPBSA.py completes successfully
> &general
> ligand_mask=":URA",
> receptor_mask="!:URA",
> startframe=1 ,
> endframe=8 ,
> interval=1 ,
> netcdf=1 ,
> entropy=0 ,
> keep_files=2 ,
> verbose=2 ,
> /
>
> &pb
> istrng=0.15 ,
> /
>
> nmode_istrng -> Ionic strength in M to use in nmode calculations
> &nmode
> nmode_istrng=0.15 ,
> /
>
And this is the command line I used:
$AMBERHOME/bin/MMPBSA.py -O \
> -i mmpbsa.in \
> -o FINAL_RESULTS_MMPBSA.dat \
> -cp FurD-Uracil_DPPC_rectbox.lipid14.protein+ligand.prmtop \
> -rp FurD-apo_ASP51_DPPC_rectbox.lipid14.protein.prmtop \
> -lp Uracil.prmtop \
> -y NETCDF FurD-Uracil_DPPC_rectbox.lipid14.cMDrun20.protein.nc \
> -yr NETCDF FurD-apo_ASP51_DPPC_rectbox.lipid14.cMDrun5.protein.nc \
> -yl NETCDF Uracil.nc
>
I can share trajectories and topologies if necessary.
Thanks in advance,
Thomas
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===============================================================
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*
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Received on Tue Sep 16 2014 - 08:00:03 PDT
