On Thu, May 27, 2004, Kamp, Marc vander wrote:
>
> For GAFF atom type assignment I noticed that atomtype/antechamber correctly
> assigns the atom type pairs in conjugated systems (e.g. the ce/cf types in
> octaquatrene (octene-chain with four conjugated double bonds, molecule 3 in
> figure 1b in the GAFF-paper), although the second atom type of the pairs
> cc/cd, ce/cf, cg/ch etc. are not (and can not be) defined in the
> ATOMTYPE_GFF.DEF file. How does atomtype/antechamber assign such conjugated
> pairs?
Look around line 1837 in atomtype.c (Amber8).
>
> by the way, when I use a pdb file of the "octaquatreen" molecule (with or
> without connectivity information) directly in antechamber (for gaff atom
> type assignment), I get an error message which does not seem to be
> appropriate:
> Cannot successfully assign bond type for this molecule, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
>
You can try the "-j 5" option to get around this problem. There is some
discussion of this here:
http://amber.scripps.edu/antechamber/new.html
But it might help if you could send us the octaquatreen pdb file: I am
collecting "problem" cases to try to help Junmei figure out how we can
better avoid the messages listed above.
....thanks...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri May 28 2004 - 22:53:00 PDT
