AMBER Archive (2008)

Subject: Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Dec 16 2008 - 06:17:15 CST

Stephane,

> With the advices of Fyd, I finally obtained the RESP charges for
> Acetate. Before to complete the tutorial with the dideptide example,
> I would like to compare my results with those obtained in the
> tutorial (especially for acetate and Methylammonium). Unfortunately
> I can't find the files generated by RED-vIII.pl. where are they ?

The charges of acetate & methylammonium (small molecules) were not
computed alone. The corresponding P2N + QM output were generated only
to be involved in a 2 molecular RESP fit to generate a N- or
C-terminal fragment.

See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#5
See TABLE 1, TABLE 2 and particularly TABLE 3 if you look for the P2N
+ QM output for those small molecules.

If you look at RESP charge derivation for acetate, you will have to go
to the part dealing with terminal fragments, i.e.
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11

See Job no 18 (with metylammonium) & 19 (with acetate)
inputs are @ TABLE 19; whole data are @ TABLE 20.

As acetate (or methylammonium) is used in a two molecules RESP fit
with a dipeptide & as this small molecule is number 1 in a list of 2,
the RESP charges of acetate are fitted independetly of molecule 2 in
the directory Mol_m1 (same idea for methylammonium). The Mol_m2
directory will contain the data for the dipeptide fitted independently
of molecule 1, while the Mol_MM directory will contain the fit of the
2 molecules together i.e. for the C-terminal fragment...

For acetate see:
http://q4md-forcefieldtools.org/Tutorial/6-Charges-2conf-RBRA-4-INTER-MCC2/Mol_m1/Mol_m1-o1.mol2

Do not hesitate to ask if you have questions because this part is not
that easy. The idea is to generate different sets of charge values to
be able to do comparisons between those sets of charges, & detect
putative bad constraint between 2 different molecules...

I hope this helps.

regards, Francois

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu