AMBER Archive (2005)

Subject: Re: AMBER: Antechamber -reorders atom sequence

From: Austin B. Yongye (ayongye_at_sunchem.chem.uga.edu)
Date: Fri Apr 15 2005 - 15:12:40 CDT

Thanks for all the help and suggestions.
Austin-

>> I am using Antechamber to generate a prep file from a gaussian output
>> file.
>> Problem is that Antechamber writes a prep file with atom sequences that
>> are different from those in the gaussian output file.
>> Here is my command line input:
>> >antechamber -i ***.log -fi gout -o ***.prep -fo prepi -at amber
>
> You can also use R.E.D.-I http://www.u-picardie.fr/labo/lbpd/RED/ to
> derive the
> topology & RESP charges for your UNIT. R.E.D. use an 'initial' PDB file
> and keep
> the atom order the same in all the steps i. e. (i) geom. optimization (ii)
> MEP
> computation (iii) RESP inputs and (iv) save the _topology/RESP|ESP_
> charges in
> a final Tripos/Sybyl .mol2 file (loadable in AMBER8/LEaP).
>
> - With R.E.D.-I you can use several molecular orientations in this
> procedure
> which makes the charges highly reproducible independently of the QM
> software &
> initial structure used..
>
> - With R.E.D.-II you can associate multi-conformation & multi-orientation
> RESP
> fit which makes the charges of high quality (to be used in MD where a
> large
> conformational space is going to be explored) for chemical elements up to
> Z=35
> (different multiplicities is also handled; useful for metal complexes).
>
> - With R.E.D.-III we wrote a small program Ante-R.E.D.-III to prepare the
> 'initial' PDB file (needed by R.E.D.-III) which modifies the atom order
> (among
> many other things) and groups CH3, CH2, NH2 groupements (have to be
> identified
> in RESP charge derivation). Intra-molecular restraints are handled now in
> R.E.D.-III with multi-conformation & multi-orientation RESP fit (needed to
> be
> used for the developement of new amino-acids for instance) etc etc...
>
> Here is how to use a Tripos .mol2 file in LEaP (instead of a prep.in file)
>
> M = loadmol2 Mol_o1.mol2
> saveoff M M.off
> # M.off being the OFF library, the format which replaces the old 'prep.in'
> one...
>
> Regards, Francois
>
> --
> F.-Y. Dupradeau
> DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
> The Scripps Research Institute, La Jolla, CA, USA
> --
> http://www.u-picardie.fr/labo/lbpd/FyD.htm
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Dr. Woods' Research Group
University of Georgia
Complex Carbohydrate Research Centre
315 Riverbend Road
Athens, GA 30602

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