[gmx-users] (no subject)

Itamar Kass ikass at cc.huji.ac.il
Sun Jul 20 12:57:01 CEST 2003

    Dear all, I am trying to simulate a peptide in a DMPC bilayer.  The 
DMPC system was taken from Dr. Tieleman site (thank you Dr. Tieleman).  
Using the modification of gromacs from Dr. Graham Smith (thank you 
also) I created a hole in the lipid.  I used two runs, one with hfm+10 
and the second with hfm+100, were the base was an image of the 
protein’s surface produced using MSM.
   Later, I inserted the peptide into the lipid, and added some Na ions. 
  The problem arose when I tried to minimize the system.  The 
minimization did not crashed, but the position restrained simulation 
afterward crashed.  When I looked upon the protein structure after 
minimization, I saw that although the helix bundle structure kept, the 
amino acids are not connect any more.  Using PROCHECK I found 
non-native bond length and angles.
   I used ffgmx_lipids force field, is it O.K.?  I also activated at the 
grompp stage the –sort –shuffle flags, is it wrong?  Does Someone have 
an idea of what wrong or how can I over come the problem?

Computers are like airconditioners... They don't work well with Windows

| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: 
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