Sorry, maybe I didn't stated my worry clearly.
I'm using AmberTools 12. Here antechamber also works fine and it is
even possible to get the parameters from parmchk.
What I'm worried about, though, is with the output of acdoctor -i
threer.mol2 -f mol2:
Error: weird atomic valence (5) for atom (ID: 11, Name: C3), please check
atomic connectivity
In my understanding this shows that parameters derived
from threer.mol2, in this specific example, wouldn't be reliable because of
this error that acdoctor reports. What I was trying to do was to get an
output mol2 file from antechamber for which acdoctor doesn't find errors.
Am I just been overreacting to this acdoctor error? Do you think it is
OK to use the parameters derived from threer.mol2 for simulations?
Thank you again,
Leandro Bortot
2013/2/8 David A Case <case.biomaps.rutgers.edu>
> 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 - 11:30:03 PST
