On Sun, Jul 28, 2013 at 3:56 PM, Shashidhar Rao <shashidharr.gmail.com>wrote:
> thanks, Jason, for the very useful tips on dealing with specific waters.
>
> When I executed the mmpbsa.py script with the following command:
>
> MMPBSA.py -O -i mmpbsa_input1 -cp 3VSX_complex_changed.prmtop -rp
> 3VSX_protein_changed.prmtop -lp 3VSX_ligand.prmtop -sp
> ../SOLV/3VSX_TIP3P_NEUTRAL_10ANG.prmtop -eo energy_collection4.csv -y
> 3VSX_TIP3P_NEUTRAL_10ANG_MOLDYN_collection4.mdcrd -o
> FINAL_collection4_Results.dat -do FINAL_collection4_DECOMP_MMPBSA.dat
>
> I obtained the following console message.
> ====================================================
>
> Loading and checking parameter files for compatibility...
> /net/casegroup2p/u2/shashi/amber12casegrp/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
> warnings.warn('ligand_mask overwritten with default\n')
> sander found! Using /home/shashi/amber12casegrp/bin/sander
> cpptraj found! Using /home/shashi/amber12casegrp/bin/cpptraj
> Preparing trajectories for simulation...
> 500 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
> ==========
>
> while the calculation seems to be running, I am a little puzzled by the
> fact that the ligand tag is overridden by the default\n. Can you please
> let me know what this means? I ask this because the ligand tag I used
> (":343") is correct in that the residue number for the ligand in the
> complex is 343.
>
Did you provide a receptor_mask? Unless you provide both a ligand_mask and
a receptor_mask, MMPBSA.py will simply use its best guess.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Jul 28 2013 - 14:00:02 PDT
