AMBER Archive (2006)

Subject: AMBER: bondtype problem

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Fri Nov 24 2006 - 18:22:23 CST

Dear all,

I have the following PDB file:

---------------------------------------
ATOM 508 N CYM 33 -1.561 -6.317 13.842
 1.00 0.00
ATOM 509 HN CYM 33 -1.126 -7.189 13.578
 1.00 0.00
ATOM 510 CA CYM 33 -1.258 -5.756 15.188
 1.00 0.00
ATOM 511 HA CYM 33 -2.182 -5.536 15.703
 1.00 0.00
ATOM 512 CB CYM 33 -0.450 -6.774 15.997
 1.00 0.00
ATOM 513 3HB CYM 33 0.377 -7.130 15.404
 1.00 0.00
ATOM 514 2HB CYM 33 -1.086 -7.605 16.265
 1.00 0.00
ATOM 515 SG CYM 33 0.180 -5.991 17.503
 1.00 0.00
ATOM 516 C CYM 33 -0.446 -4.470 15.023
 1.00 0.00
ATOM 517 O CYM 33 0.607 -4.464 14.418
 1.00 0.00
TER
ATOM 832 Zn Zn 55 1.517 -7.522 18.586
 1.00 0.00
TER
END
--------------------------------------
And I want to get the Gaussian input file as
following:

$AMBERHOME/exe/antechamber -i ZN_CYM.pdb -fi pdb -o
input3.ac -fo gcrt -c bcc -nc +1 -s 2
Total number of electrons: 82; net charge: 1

Running: $AMBERHOME/exe/divcon

Running: /home/local/amber9/exe/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f
ac -p /home/local/amber9/dat/antechamber/BCCPARM.DAT
-s 2 -j 4

Running: /home/local/amber9/exe/bondtype -f ac -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC -j
full

For atom[1]:N, the best APS is not zero, exit
For atom[8]:SG, the best APS is not zero, exit
For atom[10]:O, the best APS is not zero, exit
For atom[11]:Zn, the best APS is not zero, exit
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 "/home/local/amber9/exe/bondtype -f
ac -o ANTECHAMBER_AM1BCC.AC -i
ANTECHAMBER_AM1BCC_PRE.AC -j full" in main() of
am1bcc.c properly, exit

--------------------------------------

Will you please tell me how to solve this problem?

Best regards.

Fenghui Fan

 
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