Re: AMBER: instructions for making a library file for an unusual residue?

From: FyD <>
Date: Sun, 19 Feb 2006 18:14:10 +0100

Quoting Kenley Barrett <>:

> I need to make a library file for a methylated histidine that fits the 2003
> force field. I have read the Duan et al. article, but I am inexperienced
> with making library files (and with ab initio calculations in general) and I
> am not sure how to go about things. Are there step-by-step instructions
> anywhere for how to make a library file for an unusual residue?

As I just said in my former email, a tutorial about RESP ESP charge derivation
using R.E.D. III/R.E.DD.B. should be available very soon now.

In R.E.D. III, you just have to change a line of code to generate residues
(molecule fragment) for Duan et al FF.

Here is the general strategy followed in the tutorial using R.E.D.
( output:
Initial PDB file -- R.E.D. II --> Tripos mol2 "whole molecule"
Initial PDB file -- R.E.D. III --> Tripos mol2 "whole molecule" or
                                   Tripos mol2 "molecule fragment"

The Tripos mol2 file
is used as a _precursor_ of OFF library file in LEaP (or to generate CHARMM psf
files). This OFF file is used to generate the prmtop/prmcrd files.

In LEaP:
YOUR-UNIT = loadmol2 YOUR-FILE.mol2
You define the head & tail of your residue
You define the FF atom types
saveoff YOUR-UNIT
saveamberparm YOUR-MOLECULE your-molecule.prmtop your-molecule.prmcrd

See the leaprc-mol2tooff.ff file of the project F-60 for a quite complex example
of LEaP script in R.E.DD.B.:

You should be able to find soon more simple examples in the R.E.DD.B. database
for the AIB (dimethylalanine) residue:
1) Central fragment:
2) (+)NH3-terminal fragment:
3) (-)OOC-terminal fragment:

I will put the corresponding AIB, NAIB & CAIB leaprc-mol2tooff.ff scripts in
R.E.DD.B. (should be available in one hour or so from the links provided

regards, Francois

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Received on Sun Feb 26 2006 - 06:10:05 PST
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