AMBER Archive (2008)

Subject: Re: AMBER: mm_pbsa.pl not reading parameters for nmode

From: David A. Case (case_at_scripps.edu)
Date: Tue May 06 2008 - 13:13:54 CDT

On Tue, May 06, 2008, Seth Lilavivat wrote:
>
> So I am using the MM-PBSA approach to estimate binding energy. I am
> following protocol very close to that of the tutorial on the AMBER tutorials
> page. I can't get nmode to work so that I can approximate entropy. In my
> mmpbsa file I set "NM = 1". Then here are my parameters for nmode:
>
> @NM
> MAXCYC 5000
> DRMS 1.0e-5
> DIELC 1.0
> SCEE 1.2
> CUT 99999
>
> But when I open up the nmode.in file it looks like this:
>
> File generateFile generated by mm_pbsa.pl
> &data
> ntx = 0,
> ntrun = 1, nvect = 0,
> drms = 0.0001,
> dielc = 4.0, idiel = 0,
> scnb = 2.0, scee = 1.2
> &end
> END
>
> Am I correct in observing that I am not generating the correct
> nmode.infile? When I run the mmpbsa.pl, I then get the following
> error:
>
> DIHEDRAL ANGLE ERROR: 1 90 93 102 105
> DIHEDRAL ANGLE ERROR: 2 90 93 102 105
> DIHEDRAL ANGLE ERROR: 3 90 93 102 105
> DIHEDRAL ANGLE ERROR: 59 3 6 15 75
> DIHEDRAL ANGLE ERROR: 60 3 6 15 75
> DIHEDRAL ANGLE ERROR: 61 3 6 15 75
> DIHEDRAL ANGLE ERROR: 62 189 192 201 204
> DIHEDRAL ANGLE ERROR: 63 189 192 201 204

You are going to need to run nmode by hand, until you can figure out what is
going wrong.

Do you have non-standard force field terms? The messages above should only
come when the phase of a dihdedral term is not 0 or 180, but this never
happens in the standard Amber or gaff force fields. The message above is not
really an "error", just a warning of something unusual.

I don't use the MM-PBSA script myself, and (unfortunately) its author has
moved on and is not generally able to reply to problem reports. It is
suspicious that there is no comma after the scee listing above, since you
reported that all components except 14-EEL's are the same in sander and nmode.
You should look at the output of nmode and see what it says in this regard.

...good luck...dac

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