On Fri, Feb 08, 2013, Leandro Bortot wrote:
>
> Now I tried to use the pdb files of the molecule before and after
> minimization with Gaussian03. Acdoctor doesn't detect errors directly in
> them, but after antechamber it does again.
I can't reproduce the problem. I copied your pdb file to "threer.pdb", and
tried the following:
godel% antechamber -fi pdb -i threer.pdb -fo mol2 -o threer.mol2 -c bcc
Total number of electrons: 118; net charge: 0
Running: /home/case/amber12/bin/sqm -O -i sqm.in -o sqm.out
There were no warnings or errors, and everything seems to work out fine.
Parmchk provided the missing parameters. Adding "-j 5" or "-j 4" to the
antechamber command did not make any difference.
Can you (re-)state which version of AmberTools you have? FWIW, I've attached
the "threer.mol2" file so you can see the output.
...dac
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Received on Fri Feb 08 2013 - 11:00:03 PST
