AMBER Archive (2004)

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

From: tim (tim_at_mmb.pcb.ub.es)
Date: Mon Apr 26 2004 - 09:11:08 CDT

> 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.

weired. i'd try this: take your initial structure (in pdb format i
suppose) and first delete all hydrogens.

eg:
perl -an -i -e 'print unless ($F[2] =~ /\d*H/)' tmp.pdb

then protonate your glutamines
eg
perl -p -i -e 's/GLU/GLH/' tmp.pdb

if you now run xleap and minimize the whole structure in vacuum at least
the H-clashes should be gone. check the xleap output.

if you keep having problems attach your input pdb next time

cheers

tim

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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