From: Shashidhar Rao <>
Date: Sun, 28 Jul 2013 15:56:05 -0400

thanks, Jason, for the very useful tips on dealing with specific waters.

When I executed the script with the following command: -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...
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.

thanks again for your help,
Shashi Rao

On Sun, Jul 28, 2013 at 12:00 PM, Jason Swails <>wrote:

> On Jul 28, 2013, at 9:17 AM, Shashidhar Rao <> wrote:
> > Hello Dwight,
> >
> > many thanks for your response and I apologize for not responding sooner.
> > it is good to note that strips all waters and ions by default.
> > however, in a specific situation where I wanted to retain some water
> > molecules in the active site, I would assume that I would use cpptraj? is
> > that right?
> If there are specific waters that you need, you can just set strip_mask in
> the &general section to the mask required to delete all the unnecessary
> waters and keep those you want.
> If the waters that you need to keep are different each frame, you may need
> to preprocess the trajectory using something like the "closest" command in
> cpptraj before using
> HTH,
> Jason
> _______________________________________________
> AMBER mailing list

Shashidhar N. Rao
AMBER mailing list
Received on Sun Jul 28 2013 - 13:00:02 PDT
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