AMBER Archive (2006)

Subject: Re: AMBER: antechamber for a database of organic molecules

From: FyD (fyd_at_u-picardie.fr)
Date: Sun Feb 19 2006 - 09:51:52 CST

Quoting Yogesh Sabnis <ysabnis_at_yahoo.com>:

> I have around 50 organic compounds (in pdb files) and
> I wish to calculate the prmtop and inpcrd files for
> all of them using antechamber.
> Is there a easier way to do this for all at once
> rather than taking one file at a time.

You can do it with R.E.D.-III in a single multi-molecule (with or without
multi-orientation and multi-conformation) RESP run (each molecule being or not
independent).

See for instance the W-46 project which contains 10 solvent molecules fitted
together and independently in R.E.DD.B.
(http://www.u-picardie.fr/labo/lbpd/REDDB/). W-46 which is 28 structures RESP
fit has been generated with R.E.D.-III
See http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/W-46/info.html

We also studied more complex projects. The last one involves the eight DNA and
RNA nucleosides, all fitted together (to avoid manual adaptations between the
DNA and RNA terminal fragments). This is 76 structures RESP fit...
See http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-60/info.html

I am working on a big HTML tutorial for R.E.D.-III and R.E.DD.B. It should be
done pretty soon now. Once this is done, I think we will be able to release a
beta version of R.E.D. III...

Regards, Francois

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