In the "DIFFERENCES" section of the output file, look at the bonded terms
(e.g. the BOND, ANGLE, DIHED terms) and see if they are 0. If you use a
single trajectory, they must be since the bonding pattern is remaining
unchanged. If they're not 0, it's most likely that you used incompatible
prmtop/trajectory files.
Good luck!
Jason
On Wed, Aug 18, 2010 at 7:28 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> Did you make all the topology files using the same procedures and the same
> force fields? Did you use the same pbradii? You may want to take a look at
> your leap.log files to check these procedures. There are a lot of different
> possible inconsistencies in the topology files.
>
> -Bill
>
>
> On Wed, Aug 18, 2010 at 3:56 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
> > Hi everybody,
> >
> > I've just concluded two MMPBSA calculations using the same ligand but
> > different receptor.
> >
> > Receptor 1 gives DELTA G binding = -32.9069 +/- 4.8997
> > 0.3465
> >
> > Receptor 2 gives DELTA G binding = -2456.5838 +/- 369.3755
> > 15.0797 with the following WARNINGS
> >
> > 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)!
> > Common causes include improperly used initial_traj variable or
> improperly
> > set masks.
> >
> >
> >
> > WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
> > CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE
> RELIABLE
> > (check differences)!
> > Common causes include improperly used initial_traj variable or
> improperly
> > set masks.
> >
> > The most common cause of this is inconsistent charge definitions across
> > topology files.
> >
> > How does one check for inconsistent charge definitions across topology
> > files? Any other hint in what to look for will be most useful.
> >
> > Thanks in advance
> >
> > George
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Aug 18 2010 - 07:30:06 PDT
