Re: [AMBER] parameters for Lys-sugar

From: Urszula Uciechowska <>
Date: Mon, 23 Apr 2012 12:38:24 +0200

Dear AMber users,

I run RED to get the resp charges for my Lys-sugar molecule which I will later add to the peptide (see attachment). Now I need to generate parameters however I dont really know how to start it ? is there any tutoraial for that? what force field should I use?
Thank you for any advices

Von: FyD []
Gesendet: Freitag, 20. April 2012 11:10
An: AMBER Mailing List
Betreff: Re: [AMBER] P2N file error from RED

Dear Urszula,

> I have like five mol2 files which corresponds to the different
> conformations that I used I guess ...
>> I finally could run the RED without getting any errors. I had like 5
>> conformations in the P2N file and now I dont know which file represents the
>> final geometry with the resp charges?

As Per suggested the charge values are in the mol2 file format...

You used 5 conformations in a charge derivation procedure involving
multiple orientations and multiple conformations; so at the end R.E.D.
ends up with 5 mol2 files with different Cartesian coordinates and
with identical charge values. You can use one of these 5 files as the
Cartesian coordinates do not matter when one build a new FF library.

Several comments about these 5 conformations:
- I guess you have good reasons for selecting these 5 conformations...
- did you look at them? are they really different after the geometry
optimization step?
- is each of these 5 conformations representative of what you want (I
guess your input P2N file)?
(we also often exclude non-representaive hydrogen bonds)

regards, Francois

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Received on Mon Apr 23 2012 - 04:00:07 PDT
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