AMBER Archive (2004)

Subject: RE: AMBER: overlap between HE and OE in GLH

From: Yong Duan (yduan_at_udel.edu)
Date: Mon Apr 26 2004 - 12:24:32 CDT

 
My guess is that the "SHAKE" was off in either minimization or MD.
HE is a type "HO" atom which has a zero van der Waals radius. The
barrier separating it from overlapping with others is mainly the bond
term connecting it to the oxygen atom. This barrier is relatively low.
For this reason, you may like to try SHAKE (even in minimization).
 
yong
 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Hailong Lin
Sent: Monday, April 26, 2004 11:50 AM
To: AMBER HELP
Subject: AMBER: overlap between HE and OE in GLH

Hi, dear experts:
I am using amber7 working on the enzyme having protonated glutamic
acids. Minimisation and molecular dynamics, which start from better
structures, always generate the overlap between HE and OE in GLH and
make the structures worse, even though amber has some information about
GLH in the all_amino94.lib file. i was trying to correct some of the
overlap manually, but the more steps MD run, the more overlaps it got.
Do i need to form a non-standard residue named GLH? I hope not..
Or it is better to freeze the GLHs in the enzyme. If i need to freeze
the residues or some atoms in those residues, can i freeze the internal
coordinates of those atoms rather than the absolute positions in the
space. ( i may not express myself very clearly at this point. i mean i'd
like to freeze the -OOH parts of GLHs like how we freeze the bond length
and bond angles in Gaussian rather than freeze the cartesian coordinates
)
 
cheers
hailong

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