AMBER Archive (2008)

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

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Tue May 06 2008 - 12:50:18 CDT

Dear Amber Users,

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
 ....
...
...
...
... (It goes on and and on)

David Case suggested that my prmtop file was not being read in correctly but
how I am able to get reasonable energies without any errors when I don't use
normal mode (NM = 0). I would like to be able to use nmode in my MM-PBSA
calculations instead of calculating entropy separately because it makes life
easier. Anyone have any suggestions as to what might be happening? I am
using AMBER 8 by the way.

Thank you,
Seth

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu