Hello,
On Sun, May 8, 2011 at 11:43 AM, mirage . <m.o.m.live.fr> wrote:
>
> With the python version i obtain :
>
> GENERALIZED BORN:
>
>
>
> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND,
> ANGLE, AND/OR DIHED).
> CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE
> RELIABLE (check differences)!
>
This is good (in a sense). At least it is consistent with the perl script.
> [snip]
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND 0.0000 0.0000
> 0.0000
> ANGLE 0.0000 0.0001
> 0.0000
> DIHED -6.0897 0.1418
> 0.0819
>
Here is your problem. One of your dihedral terms is inconsistent between
your complex/receptor/ligand prmtop files. You may need to recreate some of
your topology files.
Use the "extractFrcmod.py" script to generate frcmod files of all of your
prmtop files. That will help you narrow down which torsion is causing
grief. If you just execute that program with no arguments, it tells you how
to use it.
After looking carefully at the offending file, make sure that you create
topology files that use the same force field (perhaps you used ff99SB to
create the complex, but ff99 to create the receptor/ligand?).
Another option is to use the ante-MMPBSA.py program that was included with
AmberTools 1.5 that will generate consistent complex/receptor/ligand
topology files from an input topology file. Just run that program without
arguments to display the usage message.
[snip]
>
> DIHED -6.0897 0.1418
> 0.0819
>
As I would expect, exact same result for PB.
>
> the input is:
>
> Input file for running entropy calculations using NMode
> &general
> startframe=1,
> endframe=3,
> # entropy=1,
> receptor_mask= ":1,:2,4",
> ligand_mask= ":3",
>
receptor_mask and ligand_mask are generally unnecessary. The only times
they are necessary is when you have multiple instances of the ligand in your
complex and you wish to treat one *other* than the last instance as the
"ligand" in MM/PBSA, or if your ligand is a non-sequential set of residues
inside your complex.
Outside of these peculiar cases, letting MMPBSA.py automatically determine
the correct receptor and ligand masks is a good form of error checking.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun May 08 2011 - 03:30:02 PDT
