AMBER Archive (2003)

Subject: Re: Mainchain.dat

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Tue May 20 2003 - 08:34:36 CDT

Hello Tang Kwa,
Junmei Wang used to have a tutorial on his web page but the link is not
working now.
The format of mainchain.dat is as follows: you specify head, tail, and
mainchain atom names. Then the capping atoms
you don't want to have in the prepin (omit). Then AMBER atom types before
and after head and tail, resp (in order to determine dihedrals). Last comes
charge of the resulting fragment.

Hope this helps,

Martin

HEAD_NAME C2
TAIL_NAME C6
MAIN_CHAIN C1
MAIN_CHAIN O5
OMIT_NAME N8
OMIT_NAME H10
OMIT_NAME C9
OMIT_NAME H11
OMIT_NAME H12
OMIT_NAME H13
PRE_HEAD_TYPE HC
POST_TAIL_TYPE O
POST_TAIL_TYPE N
CHARGE 0.0

----------------------------------------------------------------------------
---------------------------------------------------------------------------- 

----
Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem

>
> __________________________________
> Do you Yahoo!?
> The New Yahoo! Search - Faster. Easier. Bingo.
> http://search.yahoo.com