Thanks for the reply.
Does this mean in order to use Normal mode analysis one should longer simulations so that system had properly equilibrated ?
Regards,
Nitin Sharma
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, January 09, 2014 11:38 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Error Nmode entropy calculation
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 - 08:00:04 PST
