AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Sep 08 2006 - 23:05:11 CDT

Dear Fenghui,

About the charge information, your structure is not neutral because of the
phosphate atom. I never used antechamber to get the resp charges for my
system.

If u read Cornell 95 paper, they describe how they find the resp charges
for the residues (e.g., RG,RG3,RG5, etc.). They do gaussian calculations
on the nucleosides (no phosphate atom present), and use dimethylphosphate
(DMP) to create the joint points (and DMP has a -1 charge).

I think the net charge of your structure is -1. I just created the .mol2
file for this .pdb using the following command:

antechamber -fi pdb -i cAMP.pdb -fo mol2 -o cAMP.mol2 -c bcc -at gaff -nc
-1

The question is, can u use this residue in a bigger structure. I think
that if this residue is in between 2 residues, yes u can. If this residue
is on the 3' or 5' end, I dont think u can use it. In these cases, u need
to get the charges for cAMP3' and cAMP5'.

I think that the best way to get the RESP charges is to use the RESP
protocol. If I am wrong, please someone correct me. Good luck.

Best,

On Fri, 8 Sep 2006, Fenghui Fan wrote:

> 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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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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