AMBER Archive (2004)

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

From: Hailong Lin (
Date: Tue Apr 27 2004 - 09:32:47 CDT

Messagethanks yong.
Actually I have tried both of the NTC options. Neither SHAKE nor NO SHAKE works. Is it possiable to give them reasonable barriers by changing the van der waals parameters?
  ----- Original Message -----
  From: Yong Duan
  Sent: Monday, April 26, 2004 6:24 PM
  Subject: RE: AMBER: overlap between HE and OE in GLH

  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).


    -----Original Message-----
    From: [] On Behalf Of Hailong Lin
    Sent: Monday, April 26, 2004 11:50 AM
    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 )


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