AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Fri Sep 08 2006 - 22:06:49 CDT

The following is the full H PDB file:
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 1H2* CMP 1 17.119 5.249 4.849
 1.00 20.00 H
HETATM 5 C3* CMP 1 15.748 6.153 6.198
 1.00 20.00 C
HETATM 6 1H3* CMP 1 16.516 6.264 6.829
 1.00 20.00 H
HETATM 7 O3* CMP 1 14.919 5.191 6.829
 1.00 20.00 O
HETATM 8 P CMP 1 14.178 5.596 8.206
 1.00 20.00 P
HETATM 9 O1P CMP 1 13.027 4.685 8.391
 1.00 20.00 O
HETATM 10 O2P CMP 1 15.209 5.693 9.264
 1.00 20.00 O
HETATM 11 O5* CMP 1 13.628 7.073 7.918
 1.00 20.00 O
HETATM 12 C5* CMP 1 14.396 8.010 7.135
 1.00 20.00 C
HETATM 13 1H5* CMP 1 15.191 8.315 7.659
 1.00 20.00 H
HETATM 14 2H5* CMP 1 13.828 8.799 6.900
 1.00 20.00 H
HETATM 15 C4* CMP 1 14.849 7.321 5.881
 1.00 20.00 C
HETATM 16 1H4* CMP 1 13.985 7.085 5.436
 1.00 20.00 H
HETATM 17 O4* CMP 1 15.694 8.126 5.018
 1.00 20.00 O
HETATM 18 C1* CMP 1 16.489 7.239 4.241
 1.00 20.00 C
HETATM 19 1H1* CMP 1 16.205 7.216 3.282
 1.00 20.00 H
HETATM 20 N9 CMP 1 17.878 7.704 4.220
 1.00 20.00 N
HETATM 21 C8 CMP 1 18.550 8.165 3.117
 1.00 20.00 C
HETATM 22 1H8 CMP 1 18.122 8.264 2.219
 1.00 20.00 H
HETATM 23 N7 CMP 1 19.803 8.464 3.347
 1.00 20.00 N
HETATM 24 C5 CMP 1 19.967 8.202 4.695
 1.00 20.00 C
HETATM 25 C4 CMP 1 18.789 7.737 5.252
 1.00 20.00 C
HETATM 26 N3 CMP 1 18.595 7.384 6.533
 1.00 20.00 N
HETATM 27 C2 CMP 1 19.717 7.530 7.241
 1.00 20.00 C
HETATM 28 1H2 CMP 1 19.650 7.279 8.207
 1.00 20.00 H
HETATM 29 N1 CMP 1 20.917 7.963 6.845
 1.00 20.00 N
HETATM 30 C6 CMP 1 21.076 8.326 5.549
 1.00 20.00 C
HETATM 31 N6 CMP 1 22.263 8.786 5.151
 1.00 20.00 N
HETATM 32 HAC CMP 1 23.016 8.858 5.805
 1.00 20.00 H
HETATM 33 HAB CMP 1 22.400 9.059 4.199
 1.00 20.00 H

The following is full H topology file:
1 O2* 15.377 5.116 4.010 O.3 1
CMP -0.207
     2 HAA 15.251 4.195 4.379 H
   1 CMP 0.031
     3 C2* 16.303 5.826 4.816 C.3
   1 CMP 0.109
     4 C3* 15.748 6.153 6.198 C.3
   1 CMP 0.109
     5 O3* 14.919 5.191 6.829 O.3
   1 CMP -0.198
     6 P 14.178 5.596 8.206 P.3
   1 CMP 1.200
     7 O1P 13.027 4.685 8.391 O.2
   1 CMP -0.610
     8 O2P 15.209 5.693 9.264 O.2
   1 CMP -0.610
     9 O5* 13.628 7.073 7.918 O.3
   1 CMP -0.198
    10 C5* 14.396 8.010 7.135 C.3
   1 CMP 0.046
    11 C4* 14.849 7.321 5.881 C.3
   1 CMP 0.196
    12 O4* 15.694 8.126 5.018 O.3
   1 CMP -0.198
    13 C1* 16.489 7.239 4.241 C.3
   1 CMP 0.196
    14 N9 17.878 7.704 4.220 N.ar
   1 CMP 0.216
    15 C8 18.550 8.165 3.117 C.ar
   1 CMP -0.058
    16 N7 19.803 8.464 3.347 N.ar
   1 CMP -0.523
    17 C5 19.967 8.202 4.695 C.ar
   1 CMP 0.116
    18 C4 18.789 7.737 5.252 C.ar
   1 CMP 0.253
    19 N3 18.595 7.384 6.533 N.ar
   1 CMP -0.537
    20 C2 19.717 7.530 7.241 C.ar
   1 CMP -0.058
    21 N1 20.917 7.963 6.845 N.ar
   1 CMP -0.537
    22 C6 21.076 8.326 5.549 C.ar
   1 CMP 0.252
    23 N6 22.263 8.786 5.151 N.2
   1 CMP 0.040
    24 HAC 23.016 8.858 5.805 H
   1 CMP -0.015
    25 HAB 22.400 9.059 4.199 H
   1 CMP -0.015
    26 H001 17.119 5.249 4.849 H
   1 CMP 0.000
    27 H002 16.516 6.264 6.829 H
   1 CMP 0.000
    28 H003 15.191 8.315 7.659 H
   1 CMP 0.000
    29 H004 13.828 8.799 6.900 H
   1 CMP 0.000
    30 H005 13.985 7.085 5.436 H
   1 CMP 0.000
    31 H006 16.205 7.216 3.282 H
   1 CMP 0.000
    32 H007 18.122 8.264 2.219 H
   1 CMP 0.000
    33 H008 19.650 7.279 8.207 H
   1 CMP 0.000
@<TRIPOS>BOND
    1 1 2 1
    2 1 3 1
    3 3 4 1
    4 3 13 1
    5 4 5 1
    6 4 11 1
    7 5 6 1
    8 6 7 2
    9 6 8 2
   10 6 9 1
   11 9 10 1
   12 10 11 1
   13 11 12 1
   14 12 13 1
   15 13 14 1
   16 14 15 ar
   17 14 18 ar
   18 15 16 ar
   19 16 17 ar
   20 17 18 ar
   21 17 22 ar
   22 18 19 ar
   23 19 20 ar
   24 20 21 ar
   25 21 22 ar
   26 22 23 1
   27 23 24 1
   28 23 25 1
   29 3 26 1
   30 4 27 1
   31 10 28 1
   32 10 29 1
   33 11 30 1
   34 13 31 1
   35 15 32 1
   36 20 33 1
@<TRIPOS>SUBSTRUCTURE
  1 CMP 1

Will you please tell me how can you say there is one
net charge? How should we calculate the net charge?
The ANTECHAMBER says antechamber can calcualte the
charge, why we do not rely on ANTECHAMBER to make the
calculation?

After I use ANTECHAMBER get all the necessay files,
how can I combine these files with its receptor so
that I can run a sander?

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Fri, Sep 08, 2006, Fenghui Fan wrote:
>
> > My cAMP PDB file is:
> ...
> > After I check, I think the PDB file is correct.
>
> You are missing hydrogens at C2, C8, C1', C2', C3',
> C4' and C5'. Also, since
> your ligand has a net charge, you have to tell
> antechamber that as well.
> You might want to study the nucleotide residues in
> the standard amber library,
> or look at $AMBERHOME/test/antechamber/guanine, in
> order to get a better
> feeling for what antehcamber needs as input.
>
> ...dac
>
>
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