AMBER Archive (2004)

Subject: Re: AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file

From: David A. Case (
Date: Fri May 28 2004 - 16:34:45 CDT

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:

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.



================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to