AMBER Archive (2009)

Subject: Re: [AMBER] GAFF and NME, ACE terminal res

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Jul 14 2009 - 02:40:00 CDT

Dear JIomm,

> I am new to AMBER though I was going through Advanced Amber tutorial
> Tutorial 1 using dye and linker.

Be aware there are several inconsistencies in this tutorial.

> I want to make same type of residues to be protected by NMe (for C
> terminal) or ACE(N terminal). pls clarify the following:
>
> 1) can I use GAFF for these residues to be used later and making prmtop file.

This depends on the structure you are going to study. If you want to
develop a fragment // a component of a protein or a nucleic acid (i.
e. a modified nucleotide or unusual amino acid), you should not use
GAFF & you should use ff99SB (or ff03; for proteins only).

If your structure is organic you could indeed use GAFF.

> 2) I cannot use other than HF/631-G* method to optimise. the charges
> that I will use, during RESP fit, for NMe and ACE (as given in
> tutorial) are actually derived by optimising amino acids by HF/631-G*
> method also.

Just forget it: the HF/6-31G* or HF/6-31G** theory level (TL) was used
in the Amber force field topology databse construction. You do not
need MP2 correction or DFT in the particular cases presented.

> but for GAFF parameters have been derived by using MP2/631-G (will this
> effect the charges so derived by HF method during simulation). this is
> confusion pls clarify it whether I can use GAFF or not or  I have
> misunderstood the things

Do not mix up the TL used in force field paremeter developement & that
used in charge derivation. Here, we talk about charge derivation and
using HF/6-31G*//HF/6-31G* (or HF/6-31G*//HF/6-31G**) is perfect for
GAFF or ff99SB; [for ff03 you need to use B3LYP/cc-pVTZ
SCRF(IEFPCM,solvent=Ether)//HF/6-31G**]

For ff99SB or more generally ff94, please read:
Cieplak et al. Application of the multimolecule and
multiconformational RESP methodology to biopolymers: Charge derivation
for DNA, RNA, and proteins. J. Comput. Chem. 1995, 16, 1357.

For ff03, see:
Duan et al. A Point-Charge Force Field for Molecular Mechanics
Simulations of Proteins Based on Condensed-Phase Quantum Mechanical
Calculations. J. Comput. Chem. 2003, 24, 1999.

Finally, I suggest you to read as well:
http://q4md-forcefieldtools.org/Tutorial/ where charge derivation is
carried out accordingly to what was done in the Amber force field
topology database (Cieplak et al. J. Comput. Chem. 1995, 16, 1357).

regards, Francois

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