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
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Received on Wed May 07 2008 - 06:07:44 PDT
