[gmx-users] Energy min problem

Xavier Periole x.periole at chem.rug.nl
Thu Oct 14 09:55:06 CEST 2004

Sean Cory wrote:

>I am running energy minimalization on a protein in water. This protein has 
>protonated GLU amino acids (GLUH added with -GLU option) 
>When I try to minimize the system, it seems fine at first, but eventually the 
>H+ atom begins to move towards the OY atom in the GLU creating huge forces 
>dut to the very short distances.
There is no OY atom in a GLUH or any other residue !!!
An idea: you can choose the Oxygen atom you want to put the hydrogen on.
Just change its name in the pdb file you give to pdb2gmx.

Hope it helps


   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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