Dr. Ramón Garduño-Juárez wrote:
Dear All:
I am trying to build a lipid bilayer made of DMPC
(Dimyristoylphosphatidylcholine) surrounding a putative membrane
channel. Everything goes well until I come across with the use of
pdb2gmx and further on to the use of gromp, where I realized that I need
to add some information about DMPC, information that is supposed to be
in the rtp format.
Using an .rtp is an unnecessarily laborious (and indirect) way to add a lipid
topology. Simply #include an .itp file. You haven't said what force field
you're trying to use, but for Gromos force fields, you can use the topology from
Tieleman:
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
There are probably topologies out there for CHARMM, as well, but I don't have
the link handy.
I have no idea how to build such rtp file for DMPC. I have read and
practiced with all tutorials about the construction of lipid bilayer
with GROMACS. I have also read the relevant information about rtp files
in the GROMACS Manual. However, I still cannot figure out how to do this.
The procedure you're looking for is nearly identical to the membrane protein
topology. The only difference is the lipid :)
I will appreciate very much any help provided. I am stuck and would like
to learn how to create an rtp file from scratch, which I am sure I need
to do more than once during this project...
Investing time in an .rtp file is probably not useful here, but if you're intent
on doing it, simply read through the .rtp file for your force field and see how
the existing building blocks are built. If I were you, I would not waste my
time doing so.
-Justin
Much obliged,
Ramon Garduno
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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