AMBER Archive (2004)

Subject: Re: AMBER: pdb in RED

From: FyD (fyd_at_u-picardie.fr)
Date: Thu May 27 2004 - 14:16:59 CDT

Dear Gustavo Pierdominici Sottile,

> I am reading the manual and there are two examples with different
> definitions for hydrogen atoms. My questions is : should and hydrogen
> have the same number as the atom that it is linked, if that atom is an
> heteroatom or a carbon (non methyl, or methylene)?

YES

If you want to follow the published way to derive RESP charges:
- Equivalence of CH2 & CH3 group are carried out in the 2nd RESP stage
- All other types of equivalence implying hydrogens are carried out in the 1st
RESP stage.

The automatic generation of RESP inputs in R.E.D. is based on the PDB atom
names.

Example: CH3-NH2
CH3 equivalenced in the 2nd RESP input
NH2 equivalenced in the 1st RESP input

=> Atom names for methylamine:
CH3 = CT1 H1 H1 H1, "T" allows equivalencing in the 2nd RESP input.
NH2 = N2 H2 H2, no "T" => equivalencing in the 1st RESP input.
or
CH3 = CT999 H999 H999 H999
NH2 = N2 H2 H2

In the second R.E.D. version 2.0, RESP input generation has been updated to make
this more convenient and in particular to allow the generation of non-standard
RESP inputs...

Regards, Francois

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm
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