AMBER Archive (2009)

Subject: Re: [AMBER] ATP and GTP parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Sep 03 2009 - 03:35:11 CDT

Eduardo,

> Oh my!, do you have both?.

-1- read Cieplak et al. Application of the multimolecule and
ulticonformational RESP methodology to biopolymers: Charge derivation
for DNA, RNA, and proteins. J. Comput. Chem. 1995, 16, 1357-1377.
-2- learn how to use R.E.D.-III.x using
http://q4md-forcefieldtools.org/Tutorial/
-3- use R.E.D. Server with R.E.D.-IV
=> Everybody can generate such a complex force field topology database
where all the computational conditions are defined (orientations,
conformations, QM theory levels, charge fit with a minimum number of
charge constraints, etc...) - & without manual charge "arrangement"...

The difference between 2 protonate states is simply one additional
building block + one additional contraints between two building blocks.

> This is even better both states are great, although I will try first -2.
> I basically need to bind. ATP, ADP, GTP, GDP, AMP /GMP is not so useful
> now, but if you have them do share.

ok

> which paper do I quote?.

Data are going to be submitted in R.E.DD.B.
You will have a R.E.DD.B. code. (similar to a PDB code)
See http://q4md-forcefieldtools.org/REDDB/faq.php#3

regards, Francois

> FyD wrote:
>> Eduardo,
>>
>>> I was wondering if anyone can supply parameters for the phosphates XYP
>>> with X={A,G}, Y={T,D,M} other than those
>>> found in http://www.pharmacy.manchester.ac.uk/bryce/amber
>>> I heard somebody has the parameters compatible with ff03, would you
>>> care to share those?
>>
>> ok no problem.
>>
>> Do you need dexoxyribose or ribose ?
>> Which protonation state for each terminal phosphate ? -2 or -1 ?
>>
>> regards, Francois

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