Thanks a lot case,
I was able to figure out the problem. The problem
was with the .pdb file created (using gaussian) it seems.
It was not in the exact format as that given the test directory, after
formatting it to the required style of pdb file I was able to create the
prmtop and inpcrd files. Thanks for the suggestions. Also the units of
energy obtained in the minimisation runs are kcal/mol right?.
with regards,
Chidambar
On Tue, Sep 6, 2011 at 6:07 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Sep 06, 2011, Chidambar Kulkarni wrote:
>
> > > bta = loadMol2 BTA.mol2
> > Loading Mol2 file: ./BTA.mol2
> > Reading MOLECULE named
> ^^^^^
>
> This looks bad...the code didn't pick up the molecule name.
>
> > > list
> > gaff mods
>
> This also looks bad: there is no "bta" entry.
>
> How did you create the BTA.mol2 file? Compare it to a file like
> $AMBERHOME/AmberTools/test/antechamber/tp/tp.mol2.save.
> If you can't figure out the problem, you might post your mol2 file.
>
> ...dac
>
>
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>
--
Chidambar k
Int.PhD
JNCASR
Bangalore
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Received on Tue Sep 06 2011 - 07:00:03 PDT
