AMBER Archive (2005)

Subject: Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jul 06 2005 - 22:18:46 CDT

Dear AMBER users,

After analyzing the examples again, I think I can answer some of the
questions I asked.

> After the 6th area, I could not understand the rest of the lines. Here is
> the copy of those lines used in this sample:
>
> 6 0.000
> 1 6 1 14 2 2 2 3 2 4 2 5
> 6 0.000
> 1 1 1 9 2 10 2 11 2 12 2 13
>

Here, there are 2 constraints defined. As a result, this will find the
charges for the DX residues (as it is described in Qing Zhang's paper,
pp.3, and X stands for C,G,A,T). The first line says that there are 6
atoms which the charges of these atoms will add up to zero. The next
line describes the atoms of the previously defined constraint. '1
6' means the 6th atom in the first molecule. After numbering all of the
atoms in this sample molecule, 6th atom in the 1st molecule is the O5' of
the nucleotide. '1 14' means the 14th atom of the 1st molecule, and this
is the hydrogen bonded to the O5' atom. '2 2' means the 2nd atom in
the 2nd molecule, which is the carbon atom bonded to the O5' atom in the
2nd molecule (DMP). And the rest are the hydrogens bonded to this carbon.

The 3rd line is the second charge constraint, and the 4th line descibes
which atoms these are.

After figuring this out, I have a couple of other questions:

1. Because the gaussian output files were not given in the website
(http://monod.biomath.nyu.edu/~qzhang/Research.htm), and because it takes
a week to run these gaussian jobs (as it is stated in the paper), I could
not run the 'resp' program to see the charge results. Now, after running
'resp' we will have RESP charges for the nucleotide and DMP molecules. How
are we going to decide what the charges for DX is? Are we going to use the
O3', O5', P, O1P, O2P charges from DMP molecule as the charges for missing
atoms in the DX molecule?

2. The above procedure is done for finding DX charges. If we want to find
the DX3' or DX5', how should we define the resp input file? I would
expect to use just one constraint (as it is stated in Qing Zhang's
paper).

3. In the above protocol, on the second resp stage, CH2 and CH3 parts of
the nucleoside is refit, not the CH3 part of the DMP molecule. Why? Is it
because we have already constrained those CH3 parts in the first resp fit?
If that is so, how should we treat the DX3' and DX5' cases? In both these
cases, we will use just one constraint. Does that mean that we should
refit the CH3 part of the DMP molecule, too, which was not used on the
first resp fit?

4. And again, after the 'resp' calculation, how should we define the
missing charges in either DX3' and DX5'?

5. I still do not understand the 8th and 9th parts of the 'resp' input
file; intermolecular charge constraints and multiple molecule atom
equivalencing.

Thanks in advance.

Best regards,

> Best,
>
> PS:
>
> The structure of DMP is as follows:
>
> O1P
> |
> CH3 - O3' - P - O5' - CH3
> |
> --- O2P ---
> II IV
>
> The structure for the cytidine is as follows:
>
> | HO
> III | \
> | O5'
> |
> C5' O4' BASE
> \ / \ /
> C4' C1'
> \ /
> C3' - C2'
> |
> O3' |
> \ | I
> H |
>
> PS: I skipped the relevant hydrogens. 

-- 
  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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