[gmx-users] DMPC bilayr

Itamar Kass ikass at mail.ls.huji.ac.il
Mon Jan 13 20:02:16 CET 2003

   Dear fellows, I am trying to use some of the files taken from Dr. Tieleman
homepage without any successful.  I downloaded the files lipid.itp and copied
the entries under atomtypes and nonbond_params to the relevant sections in
ffgmxnb.itp.  I also download dmpc.itp in order to use the almN4start.pdb
structure (in which I think there is DMPC bilayr).
   I entered my pepteid using InsightII V.98 creating the file merged.pdb and
used "editconf -f merged.pdb -o start.gro" to create a .gro file in which I
changed all the POP molecules into DMPC molecules.  Then I used "pdb2gmx -f
start.gro -p merged.top -o merged.gro -ignh" (with the OPLS-AA/L all-atom force
field) to produced the files neede. The program responded was "Atom C in residue
DMSO 1 not found in rtp database".
   Does someone know how to solve it?  Thanks you for your help, Kass.

| 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 vms.huji.ac.il
| Group Homepage: http://www.ls.huji.ac.il/~membranelab/
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