AMBER Archive (2006)

Subject: AMBER: Problem in Antechamber

From: Sai Kumar Ramadugu (compchem123_at_gmail.com)
Date: Tue Jan 10 2006 - 05:17:53 CST

Dear Amber users,
    I want to simulate a Drug-DNA complex. The complex has
acridine-peptide (N-alpha(9-acridinoyl)-tetraarginine). When I'm
trying to make a prepin file and frcmod file by giving command
   antechamber -i acridine.pdb -fi pdb -o acridine.prepin -fo prepi -c
bcc -s 2, the following report is being generated

Running: /home/gourmet/amber/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 650; net charge: 0

Running: /home/gourmet/amber/amber8/exe/divcon

Running: /home/gourmet/amber/amber8/exe/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/home/gourmet/amber/amber8/dat/antechamber/BCCPARM.DAT -j 4

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

Running: /home/gourmet/amber/amber8/exe/atomtype -i
ANTECHAMBER_PREP.AC0 -o ANTECHAMBER_PREP.AC -p gaff

Running: /home/gourmet/amber/amber8/exe/prepgen -i ANTECHAMBER_PREP.AC
-f int -o aflo.prepin -rn " C " -rf molecule.res

The prepin created doesnot have atom names. I changed the value of
MAXVASTATE in define.h and recompiled but I dont know how to do the
change in APS.DAT.
  Can anyone help me in this regard?
Thanks and regards,
    Sai
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