> 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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Received on Fri Apr 15 2005 - 17:53:00 PDT
