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
>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Aug 18 2010 - 04:30:03 PDT
