AMBER: five-coordinated phosphorus

From: Smooth Cutie <>
Date: Fri, 16 Nov 2007 17:48:40 -0600


I need to include a five-coordinated phosphorus compound in my simulations. The geometry and esp were calculated by using Gaussian 03. But when I tried to prepare the prepin file, antechamber failed to generate ac files.

The error message is:
Warning: the assigned bond types may be wrong, 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
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/opt/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit

I tried to edit the APS.DAT but I really don't understand the meaning of the columns in the file. I don't need to add a new atom type to the gaff. I can create a seperate force field file on my own. I only need the prepin file even if the atom type for the five-coordiated phosphorus is the same as that for phosphate.

Any advice?


Yubo Fan
Chemistry Dept.

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Received on Sun Nov 18 2007 - 06:07:54 PST
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