AMBER Archive (2006)

Subject: AMBER: a ligand file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Fri Sep 08 2006 - 20:31:59 CDT

My cAMP PDB file is:

HETATM 1 O2* CMP 1 15.377 5.116 4.010
 1.00 20.00 O
HETATM 2 HAA CMP 1 15.251 4.195 4.379
 1.00 20.00 H
HETATM 3 C2* CMP 1 16.303 5.826 4.816
 1.00 20.00 C
HETATM 4 C3* CMP 1 15.748 6.153 6.198
 1.00 20.00 C
HETATM 5 O3* CMP 1 14.919 5.191 6.829
 1.00 20.00 O
HETATM 6 P CMP 1 14.178 5.596 8.206
 1.00 20.00 P
HETATM 7 O1P CMP 1 13.027 4.685 8.391
 1.00 20.00 O
HETATM 8 O2P CMP 1 15.209 5.693 9.264
 1.00 20.00 O
HETATM 9 O5* CMP 1 13.628 7.073 7.918
 1.00 20.00 O
HETATM 10 C5* CMP 1 14.396 8.010 7.135
 1.00 20.00 C
HETATM 11 C4* CMP 1 14.849 7.321 5.881
 1.00 20.00 C
HETATM 12 O4* CMP 1 15.694 8.126 5.018
 1.00 20.00 O
HETATM 13 C1* CMP 1 16.489 7.239 4.241
 1.00 20.00 C
HETATM 14 N9 CMP 1 17.878 7.704 4.220
 1.00 20.00 N
HETATM 15 C8 CMP 1 18.550 8.165 3.117
 1.00 20.00 C
HETATM 16 N7 CMP 1 19.803 8.464 3.347
 1.00 20.00 N
HETATM 17 C5 CMP 1 19.967 8.202 4.695
 1.00 20.00 C
HETATM 18 C4 CMP 1 18.789 7.737 5.252
 1.00 20.00 C
HETATM 19 N3 CMP 1 18.595 7.384 6.533
 1.00 20.00 N
HETATM 20 C2 CMP 1 19.717 7.530 7.241
 1.00 20.00 C
HETATM 21 N1 CMP 1 20.917 7.963 6.845
 1.00 20.00 N
HETATM 22 C6 CMP 1 21.076 8.326 5.549
 1.00 20.00 C
HETATM 23 N6 CMP 1 22.263 8.786 5.151
 1.00 20.00 N
HETATM 24 HAC CMP 1 23.016 8.858 5.805
 1.00 20.00 H
HETATM 25 HAB CMP 1 22.400 9.059 4.199
 1.00 20.00 H
CONECT 1 2 3
CONECT 2 1
CONECT 3 1 4 13
CONECT 4 3 5 11
CONECT 5 4 6
CONECT 6 5 7 8 9
CONECT 7 6
CONECT 8 6
CONECT 9 6 10
CONECT 10 9 11
CONECT 11 4 10 12
CONECT 12 11 13
CONECT 13 3 12 14
CONECT 14 13 15 18
CONECT 15 14 16
CONECT 16 15 17
CONECT 17 16 18 22
CONECT 18 14 17 19
CONECT 19 18 20
CONECT 20 19 21
CONECT 21 20 22
CONECT 22 17 21 23
CONECT 23 22 24 25
CONECT 24 23
CONECT 25 23
END

After I check, I think the PDB file is correct.
However I still cannot get the necessary files with
ANTECHAMBER. The error is as I told you before:
$AMBERHOME/exe/antechamber -i cAMP.pdb -fi pdb -o
cAMP.prepin -fo prepi -c bcc -s 2

Running: /home/local/amber9/exebondtype -i
ANTECHAMBER_BOND_TYPE.ACO -o ANTECHAMBER_BOND_TYPE.AC
-f ac -j full

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 MAXUTOFF 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/localamber9/exebondtype -i
ANTECHAMBER_BOND_TYPE.ACO -o ANTECHAMBER_BOND_TYPE.AC
-f ac -j full: in judgebondtype () of antechamber.c
properly, exit

Will you please tell me how to solve it?

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

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