Re: [AMBER] I got a error

From: Jason Swails <>
Date: Fri, 13 Dec 2013 12:10:14 -0500

Some general advice about asking questions first: This question was
difficult and time-consuming to answer. Nothing was actually asked, you
didn't say exactly what you did, and you provided only starting files
rather than input files and scripts. Answering this required me to
guess the commands, programs, and input files you used to go from the
PDB files to the error message. I will always answer 'good' questions
first ['good' as defined here:] and will put off
vague, time-consuming questions until I have more time (which increases
the chance of the question being forgotten about).

When asking questions about problems with running, for
instance, you should provide all input files you used (any trajectories
should be trimmed to as few frames as possible that still reproduce the
error), and provide the command you used (pasting the exact output you
received, including the context of any error messages, also helps).

That said, my answer is below.

On Fri, 2013-12-13 at 18:42 +0800, David Chen wrote:
> I got a error when I use Alanine Scanning to compare to the binding energy
> of two protein.

I could not reproduce your problem. However, since you did not give me
the files you used with or the commands that you used, I could
only guess.

Here is what I did:

I used tleap to create a topology file from complex.pdb and
complex_mutate_tyr278.pdb (since there were only amino acid residues, I
only had to load the PDB files and save the topology files). The script
I used was:

source leaprc.ff12SB
l = loadPDB complex.pdb
k = loadPDB complex_mutate_tyr278.pdb

saveAmberParm l complex.parm7 complex.rst7
saveAmberParm k mutant.parm7 mutant.rst7

Then I used to create a receptor and ligand topology file
using the receptor mask :1-494: -p complex.parm7 -r receptor.parm7 -l ligand.parm7 -m
":1-494" -p mutant.parm7 -r mutantr.parm7 -l mutantl.parm7 -m

Then I ran with the following input file (
&alanine scanning

using the following command-line: -i -cp complex.parm7 -rp receptor.parm7 -lp
ligand.parm7 -mc mutant.parm7 -mr mutantr.parm7 -y complex.rst7

The resulting output from was:

bash $ -cp complex.parm7 -mc mutant.parm7 -y complex.rst7 -i -mr mutantr.parm7 -rp receptor.parm7 -lp ligand.parm7

Loading and checking parameter files for compatibility...
mmpbsa_py_energy found!
Using /home/swails/build_amber/amber/bin/mmpbsa_py_energy
cpptraj found! Using /home/swails/build_amber/amber/bin/cpptraj
Preparing trajectories for simulation...
Mutating trajectories...
1 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations
with /home/swails/build_amber/amber/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Running calculations on mutant system...

Beginning GB calculations
with /home/swails/build_amber/amber/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  no mutation found in ligand; using unmutated files

Total setup time: 10.545 sec.
Creating trajectories with cpptraj: 0.271 sec.
Mutating trajectories: 0.472 sec.
Total calculation time: 46.050 sec.

Total GB calculation time: 46.050 sec.

Statistics calculation & output writing: 0.004 sec.
Total time taken: 57.347 sec. Finished! Thank you for using. Please cite us if you publish
this work with this paper:
   Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N.
Gohlke, H. and Roitberg, A. E.
   J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321

Hopefully you can find what you did wrong by comparing your workflow to

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Dec 13 2013 - 09:30:02 PST
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