AMBER Archive (2006)

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

From: Kenley Barrett (
Date: Mon Feb 20 2006 - 18:22:22 CST


Thank you very much for your reply. I'm afraid that I'm still confused about
what I need to do. Can R.E.D or R.E.D. II match the Duan et al. 2003 force
field, or do I need R.E.D. III to match the 2003 force field? If I need
R.E.D. III, is it available for downloading yet? Does it have a manual
online? I was only able to find information on your website relating to
R.E.D. and R.E.D. II.

You mentioned that you had discussed the making of library files in a former
e-mail--I'm afraid I wasn't able to find this e-mail. If I'm asking
questions that you have already answered, could you please refer me to the
date of that e-mail? I apologize if I'm wasting your time asking questions
that have already been answered.

Please let me know any clarification that you can offer regarding my
questions. Thank you very much for your help.


On 2/19/06, FyD <> wrote:
> 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"
> or
> 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
> quit
> 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
> above).
> regards, Francois
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