Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids

From: David A Case <>
Date: Wed, 26 Aug 2015 08:33:02 -0400

On Wed, Aug 26, 2015, wrote:
> I checked the trajectory through the cpptraj 'check' command and found no
> issue. I tried to run with the serial version also, it is giving the same
> error as printed bellow.
> line 661, in _get_energies
> ValueError: invalid literal for float(): *************

This message says that the program found "****" (i.e. a number too large to
print in the requested area) for the van der Waals energy for some snapshot.
Look through your output files by hand to see if you can see what is
happening. Double-check all your filenames: one explanation for the behavior
is that the prmtop file and the trajectory file are not paired up correctly.

This is probably something that is going to be very difficult to debug
remotely. If you can't get clues by looking through the MM-PBSA output files,
you will have to do some calculations "by hand", just selecting snapshots and
computing their energies (i.e. *not* using the superstructure).


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Received on Wed Aug 26 2015 - 06:00:04 PDT
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