On Fri, Feb 20, 2015 at 8:24 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Fri, Feb 20, 2015, Shreeramesh wrote:
> >
> > I attached the "lig.mol2: file which contains two chlorine atom. While
> > running tleap "lig.mol2" was combined with another ligand "lig2.mol2".
>
> The mol2 files you have use Tripos atom types, which will not be known to
> Amber. Actually, I can't figure out how the tleap script you attached
> could
> possibly have worked. (Maybe there is lots of stuff in the lig.frcmod file
> that I am not expecting).
>
> (One wild guess: the tleap script refers to LIG.mol2, whereas the file you
> attached to your email was named lig.mol2. Did you attach the wrong files?
> Try to construct a minimal example [just one ligand, one operation] that
> illustrates the problem.)
>
In the OP's defense, if he is using Mac OS X, his filesystem is likely
case-insensitive, so this should work. But it wouldn't be portable
cross-platform...
>
> (Developers: we should try to detect Tripos atoms types upon loading a mol2
>
> file in tleap, and output an approriate warning message to the user.)
>
What would we do with said atom types? Can you clarify what problem this
is causing?
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 20 2015 - 06:00:04 PST
