On Sat, Jun 22, 2013, Krisztina Feher wrote:
> Sorry, that was my first failed attempt. I attached a correct pdb
> file. The CO carbon is assiged as "c2" by divcon and as "c1" by sqm in
> the output .mol2 file.
This is still a very odd structure. The NZ nitrogen in one residue
(DAP) is charged (NH3), but the equivalent position on the neighboring
residue (IGC) is not (NH2). The "alanine" is terminated as an aldehyde
residue. It would be better to use ACE and NME capping groups, as
Francois suggested.
The IGC residue is badly formed: there are two atoms named HT1, and then
the "HT2" proton listed in the pdb file as part of the Alanine residue is
actually part of IGC. If I remove the duplicate atom names and put the
dangling HT2 proton in the proper residue, antechamber assigns "correct"
atom types, with all the carbonyl carbons as "c:.
Notes:
1. As noted before, divcon vs sqm is irrelevant. You can save a lot of time
by leaving off the "-c bcc" flag, while experimenting to get your molecule
put together correctly. Getting "bad" atom types sometimes reflects a bug
in antechamber, but more often (as here) reflects errors in the input
structure.
2. Accerlrys Discovery Studio really seems to be putting out bad structures.
[I can't tell if this is the fault of the program, or of the way you used the
program....] You'll have to spend time examining things very carefully by
hand. In particular, your structure for IGC is unlikely to be the one you
really want. For charge and parameter development, I'd suggest tackling IGC
and DAP in separate steps, and not try to combine two non-standard residues
into a single structure.
3. It is also true that antechamber doesn't give especially good informative
messages when it gets into trouble. (Requiring "good" input is a common
feature of much academic software). In Junmei's defense, it would take a lot
of chemical intuition (encoded as artificial intelligence, I guess) to figure
out what was wrong with the structure you provided. Just continue to be
careful, and look closely at all your outputs.
...dac
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Received on Sat Jun 22 2013 - 10:00:02 PDT
