AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Sep 08 2006 - 21:23:48 CDT

Dear Fenghui,

I am not a chemist, but I tried to understand the bonding of your
structure. I think the net charge is not zero. Also, are u sure there
arent any other H-atoms present?

Best,

On Fri, 8 Sep 2006, Fenghui Fan wrote:

> 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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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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