On Thu, 2014-01-09 at 14:39 +0800, Nitin Sharma wrote:
> Dear amber users,
>
> I have successfully calculated entropy using Quasi Harmonic BUT using same files I am getting error in N-mode
>
> Input file for running entropy calculations using NMode
> &general
> endframe=2000, verbose=1,netcdf=1,
> /
> &gb
> igb=2, qm_theory = 'PM3', saltcon=0.100
> /
> &nmode
> nmendframe=5,
> nminterval=2, nmode_istrng=0.1,
> /
>
>
> Error
> /hpctmp/a0068362/amber12/bin/cpptraj: /app1/common/Compiler/gnu/gcc-4.7.2/lib64/libstdc++.so.6: no version information available (required by /hpctmp/a0068362/amber12/bin/cpptraj)
> Line minimizer aborted: step at upper bound 0.087707226
> Line minimizer aborted: step at upper bound 0.060636546
> Line minimizer aborted: step at upper bound 0.001947199
> Line minimizer aborted: step at upper bound 0.0034249663
> Line minimizer aborted: step at upper bound 0.00020112081
> Line minimizer aborted: step at upper bound 0.0015247798
> Line minimizer aborted: step at upper bound 0.0075415201
> Line minimizer aborted: step at upper bound 0.015369098
> Line minimizer aborted: step at upper bound 0.00027678326
> Line minimizer aborted: step at upper bound 0.0090360341
> Line minimizer aborted: step at upper bound 0.0017591125
> CalcError: /hpctmp/a0068362/amber12/bin/mmpbsa_py_nabnmode failed with prmtop complex.prmtop!
It seems like the XMIN minimizer is failing. The only thing I can
suggest is to pre-minimize all of the snapshots using sander and imin=5
(see the manual for details). You can then use the minimized trajectory
and feed that to MMPBSA.py (although the minimized trajectory will not
be useful for GB and PB calculations).
> Also can someone guide me regarding the choice between N-mode and Quasi Harmonic. Which one of them is a better choice to calculate entropy considering accuracy and also time
Both have strengths and (probably quite a few more) weaknesses. Normal
mode calculations will undoubtedly take much, much longer to finish, but
will also converge with far fewer snapshots.
Computing entropies is inherently difficult to do accurately, and there
is a lot of literature devoted to the topic.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 09 2014 - 08:00:03 PST
