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<blockquote type=cite class=cite cite>1) Which is the best force field to
use for a DMPC bilayer?</blockquote><br>
Probably either OPLS-AA or G43a2.<br><br>
<blockquote type=cite class=cite cite>2) If i used the DMPC.itp from Dr
Tieleman s site, where do i need to save it in<br>
order for the pdb2gmx,edit conf etc to work....that is, do i need to save
it in<br>
the "top" folder or do i need to place it in the specific
forcefield file for<br>
it to work?</blockquote><br>
The *.itp file is used in the simulation steps (whether that is energy
minimisation, restrained simulation and full run). So it only has
to be in the paths or the current working directory.<br><br>
<blockquote type=cite class=cite cite>3) How do i create a DMPC.top file
and DMPC.gro file? (I mean are there any<br>
DMPC.pdb files out there?)</blockquote><br>
For the .top file, see the manual. For the .gro file, if you want a
single molecule, you can just take the .gro file for the membrane and
copy out a single molecule from that.<br><br>
<blockquote type=cite class=cite cite>4) I tried using pdb2gmx on Dr
Tieleman s DPPC64.pdb,and ended up getting 26<br>
(A-Z) posre.itp files and DPPC_A.itp -DPPC_Z.itp(ANother 26).Is it
necessary to<br>
create all these files seperately? BUt since there are 64 lipids, what
about<br>
the other lipids? Is it necessary to create posre files for every
individual<br>
lipid? </blockquote><br>
You only need one posre file for each type of molecule, not for each
molecule.<br><br>
<blockquote type=cite class=cite cite>5) Are there any good resources out
there which describe how to setup a bilayer<br>
simulation,Since i am working this out all on my own, i dont have anyone
to<br>
discuss this with.</blockquote><br>
Search this emailing list, has been discussed in various manners for some
time. Plus read any publications to find out how others are doing
things.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Lecturer<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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