[gmx-users] terminate sugars

Glenn Johnson gjohnson at srrc.ars.usda.gov
Tue Mar 22 17:14:18 CET 2005

On Tue, 2005-03-22 at 11:25 +0300, Andrey V. Golovin wrote:

> Hello Glenn,
> I think the only solution is to create a new block (end residue), but
> you can try to use termini database.

Okay, how would I properly adjust the charges so that the molecule is
neutral with the additional atoms?  Looking at the charges on the atoms
involved from the GLCA building block would leave me with a charge of
0.038 after adding two hydrogens and an oxygen.

> Glenn Johnson> I am using the GLCA sugar building
> Glenn Johnson> block from ffG43a1.rtp and am not
> Glenn Johnson> sure how to terminate the ends.  I need
> Glenn Johnson> an H on O4, an O1 on C1 and an H
> Glenn Johnson> on the O1 to make a complete sugar
> Glenn Johnson> unit.  How would I add these atoms?
> Glenn Johnson> Thanks.

Glenn Johnson <gjohnson at srrc.ars.usda.gov>
U. S. Department of Agriculture

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