AMBER Archive (2005)

Subject: Re: AMBER: please help us on partial charge calculation of PT complex using RESP

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Jul 01 2005 - 11:07:40 CDT

Quoting peng79_at_email.unc.edu:

> We are trying to conduct ab initio calculation for the partial point charges
> of a PT-DNA adduct complex. The charge of PT we obtained from RESP is out of
> our expectation. Since PT is a very high atomic number (78) heavy atom, we
> are wondering whether or not RESP could handle it. We also would like to hear
> about any advice about how to obtain the accurate partial charge for such
> heavy atom in complex. We will detail our ab initio calculation procedures
> and we would like you to help us identify any potential problems.

I do not think it has been studied...
With R.E.D.-II http://www.u-picardie.fr/labo/lbpd/RED/, you can derive RESP/ESP
charges for chemical elements up to Br (This means this already involves Zn Fe
Cu Zn elements)...

For such PT element, I think it has never been done, and the RESP strategy has
been developped mainly for bio-organic molecules... Even for Zn Fe Cu Zn, I am
not sure if an extensive study of the RESP approach has been really
performed...

> We started from available NMR solution or crystal structure and built
> [Pt(NH3)2(9meGua)2]2+ (Cisplatin) using insightII in order to simplify the
> system for following QM calculation. (See structure in attachment ?structure
> model.doc?.)
>
> Then we wrote our own Gaussian 03 input script to perform the QM calculation.
> We first performed the minimization / geometry optimization for the structure
> and then generated the molecular electrostatic potential. (See Gaussian 03
> input script in attachment ?Gaussian 03 input.doc?.)

OK, so you added a new raddi for the PT...

> Final steps, we ran espgen from AMBER 8 package to get the .esp file and it
> succeeded. espgen ?i Gaussian_03_output.log ?o filename.ESP
> Since AMBER or ANTECHAMBER program could not recognize PT atom and bonds
> bound
> to PT, we prepared our own two stage RESP input files. (See RESP input
> scripts in attachment ?RESP1.IN? and ?RESP2.IN?.)

OK

> There was no error messages
> generated and RESP completed silently. However the final charge we obtained
> is unexpected. From previous work done by other group, the charge of PT in
> the same complex is around +0.7 but we obtained -0.1.

- I would 1st check in the RESP source code if PT is handled... I do not think
so...
- Some RESP charges were derived for some heme-complexes and the RESP charges
were very strange, I would not be surprised to observe the same thing for your
PT molecule...
See Journal of Computational Chemistry Volume 25, Issue 13, Date: October 2004,
Pages: 1613-1622 Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zaida
Luthey-Schulten

> As far as our understanding, in order to let RESP run, the only necessary
> files are .ESP and two two-stage RESP input files. RESP does not need any
> information from AMBER. Thus though AMBER or ANTECHAMBER failed to recognize
> PT atom and bonds bound to PT, it should not affect RESP.

YES

> So we could claim
> RESP as a standalone program. However we guess within RESP program, it should
> be able to recognize certain atom types, like H, C and N etc, in order to do
> the right charge fitting. Thus we are wondering whether PT atom type is
> defined in RESP or not because in gaff.dat file within AMBER, S (16) is the
> largest atomic number atom defined.

look in $AMBERHOME/src/resp/resp.f

Regards, Francois 

-- 
  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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