Dear Amber users and Developers
I want to calculate per residue decomposition energy, for this I am using
MMPBSA.py module along with Amber 12. I have six systems of varying
concentration of solute. The three system which have low concentration
(also less no of atoms) run successfully, while others three systems which
have higher concentration (high atoms numbers) I am observing following
error at the last of _MMPBSA_complex_pb.mdout.0 file .
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
Cpptraj Generated Restart
begin time read from input coords = 1.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
Cpptraj Generated trajectory
minimizing coord set # 1
PB Bomb in pb_atmlist(): maxnba too short
I search this error in Amber mailing list, but I didn't found any useful
information. I given the following input file
&general
startframe=1001, endframe=2500, interval=50,
keep_files=0,
/
&pb
istrng=0.0,
/
&decomp
idecomp=4, dec_verbose=0,
/
Would any ones suggest me to resolves this problem.
Thank you in advance for your help.
Regards
Rahman
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*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
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Received on Mon Oct 27 2014 - 00:30:02 PDT
