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Dear fellows, I am trying to use some of the files taken from Dr.
Tieleman<BR>homepage without any successful. I downloaded the files
lipid.itp and copied<BR>the entries under atomtypes and nonbond_params to the
relevant sections in<BR>ffgmxnb.itp. I also download dmpc.itp in order to
use the almN4start.pdb<BR>structure (in which I think there is DMPC
bilayr).<BR> I entered my pepteid using InsightII V.98 creating the
file merged.pdb and<BR>used "editconf -f merged.pdb -o start.gro" to create a
.gro file in which I<BR>changed all the POP molecules into DMPC molecules.
Then I used "pdb2gmx -f<BR>start.gro -p merged.top -o merged.gro -ignh"
(with the OPLS-AA/L all-atom force<BR>field) to produced the files neede. The
program responded was "Atom C in residue<BR>DMSO 1 not found in rtp
database".<BR> Does someone know how to solve it? Thanks you
for your help, Kass.</FONT><BR></FONT></DIV>
<DIV><FONT face=Arial size=2>===========================================<BR>|
Itamar Kass<BR>| The Alexander Silberman<BR>| Institute of Life Sciences<BR>|
Department of Biological Chemistry<BR>| The Hebrew University, Givat-Ram<BR>|
Jerusalem, 91904, Israel<BR>| Tel: +972-(0)2-6585146<BR>| Fax:
+972-(0)2-6584329<BR>| Email: <A
href="mailto:ikass@vms.huji.ac.il">ikass@vms.huji.ac.il</A><BR>| Group Homepage:
<A
href="http://www.ls.huji.ac.il/~membranelab/">http://www.ls.huji.ac.il/~membranelab/</A><BR>============================================</FONT></DIV></BODY></HTML>