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: Thu Jul 07 2005 - 16:56:14 CDT

Dear Qing Zhang,

Thank you very much for your answers. It answered all of the questions I
needed to know.:) The only thing that still bugs my mind is the 8th and
9th parts of the resp program (or maybe I am confused a little bit). Is
the 7th part the charge constraints when the atoms are within the
molecule? For instace, when nmol=1, there can be charge constraints in
the molecule. When nmol=2 (or more), the constraints can be between 2-3
molecules (which means intermolecular). So, I would guess that in your
sample the constraints are intermolecular (which means the 8th and 9th
areas are used). Thanks a lot for your time/answers.

Best,

On Thu, 7 Jul 2005, Qing Zhang wrote:

> Dear Ilyas,
>
> Please see my answers in your message body below.
>
> > 1. 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?
>
> Yes, because the O3¡¯ group and the O5¡¯ groups in the
> nucleotide are cancelled out by the two CH3 groups of
> DMP in the two constraints. In the RESP result, you
> will see two sets of partial charges, one from the
> nucleotide and the other from DMP. You will have to
> manually pick up the right charges for these five
> atoms.
>
>
> > 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).
>
> Yes, just use one constraint for each case. For
> example (DX5), you constrain group I and II (they are
> cancelled out) in RESP, but keep the O5¡¯ group of the
> nucleotide after RESP.
>
>
> > 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?
>
> The CH3 groups in DMP will always be discarded after
> RESP, there is no need to refit them.
>
>
> > 4. And again, after the 'resp' calculation, how
> > should we define the
> > missing charges in either DX3' and DX5'?
>
> First of all, the constrained part (I or III) in the
> nucleotide and the two CH3 groups in DMP should be
> discarded. Second, the unconstrained part in the
> nucleotide is kept. Third, the phosphate group (P,
> O1P, O2P) is used in DX3 but not in DX5, because the
> latter does not have this group.
>
>
> > 5. I still do not understand the 8th and 9th parts
> > of the 'resp' input
> > file; intermolecular charge constraints and multiple
> > molecule atom
> > equivalencing.
>
> Intermolecular charge constraints is like the
> constraints between the nucleotide and DMP, such as
> I+II=0 or III+IV=0. It is similar to the 7th part.
>
> Regarding multiple molecule atom equivalencing (also
> the first question in your previous email), it is used
> to equivalence the charges of the DNA/RNA backbone
> atoms (please check Cieplak et al. 1995 for sure)
> between A, T(U), G, C. That is how AMBER partial
> charges were developed for the DNA/RNA (see Cieplak et
> al. 1995). Thus, our protocol (without this
> equivalencing) will give these atoms the partial
> charges slightly different from AMBER. To study a
> specific molecule (instead of developing the AMBER
> force field), this equivalencing is usually not used.
>
>
> Setting up RESP runs is time consuming. I also hope
> this process can be automatic in the future.
>
> Sincerely,
>
> Qing
>
> ======================================
> Qing Zhang, Ph.D.
> Research Associate
> Molecular Graphics Laboratory
> Department of Molecular Biology, MB-5
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000
> Tel: (858) 784-2202
> Fax: (858) 784-2860
> Email: qzhang_at_scripps.edu
> ======================================
>
>
>
>
> ____________________________________________________
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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