Re: [AMBER] P2N file error from RED

From: FyD <>
Date: Fri, 20 Apr 2012 11:10:02 +0200

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

AMBER mailing list
Received on Fri Apr 20 2012 - 02:30:04 PDT
Custom Search