AMBER Archive (2004)

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

From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Thu May 27 2004 - 08:01:13 CDT

Dear all,
 
I'm using antechamber (atomtype) for automatic atom type assignment of organic molecules. I'm now trying to use atomtype for assignment of the atom types found in the Quanta CHARMm force field by making my own atom type definition file.
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?
And, what's currently most important for me, is it possible to use this feature in assigning conjugated atom pairs in the Quanta CHARMm force field (i.e. CUA1/CUA2/CUA3, CR66/CS66/CQ66)?
 
Thanks for any help/information,
Marc
 
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

When I use a mol2 file instead (created directly from the pdb with vega), I don't get an error and gaff atom types are assigned correctly.
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