James Starlight wrote:
Dear Justin,
Indeed I didnt take into account square degree so all values presented
in the tutorial exactly true so this was exactly my mistake. :(
After some iterations I've obtained value for S per lipid beetween
0.65-0.71 A^2. This is the example of the system wich I've obtained
after solvation and futher minimization.
http://www.sendspace.com/file/h6urhq It looks good. :) By the way I'd
like to know about correct value for the S per protein ? Where I can
obtain such information for my protein ? ( e.g for big proteins such
receptors and channels )
Such information depends on whether there is experimental evidence for the
protein you're looking for.
The error with GenBox was due to the big vdv R for the carbons. It's
intresting that I couldnt increase this value mush as 1.2. But my
finally system didnt consist of some water within the membrane so I
supose that it's good.
Now my system on the stage of the equilibtation so I have not any
questions yet but I only wounder to know about teqnique of the force
fied preparation for the membrane protein simulation.
In this work I've done this step in accordance with the tutorial. On the
last stage I've copied gromos53a6_lipid.ff directory in $GMXLIB so now
I can use it in pdb2gmx for instance.
But when I've tried to make gro and top files for my lipid.pdb via
pdb2gmx I've obtained errors that Residue 'DPP' not found in residue
topology database so I think that in addition to the operations wich
I've already done I should also make some changes in the
/gromos53a6_lipid.ff/aminoacids.hdb
./gromos53a6_lipid.ff/aminoacids.n.tdb
./gromos53a6_lipid.ff/aminoacids.c.tdb
shouldn't I?
pdb2gmx is not suited for building topologies of multi-molecule, heterogeneous
systems like solvated membranes. You may be able to get a topology, but it will
be a redundant mess. Follow the protocol in the tutorial; it avoids these
issues in the most streamlined way possible. If you need a topology of a new
lipid, create an .rtp entry (if one does not exist already) and run pdb2gmx on a
single lipid molecule. You can then #include the new .itp file in your system
topology.
Finally, I've heard that there are already pre-build force fields for
the membrane smulation. E.g I've heard that there is some modified
CHARMM ff wich gave good results in simulation. Do you know something
about this?
Various CHARMM parameter sets exist. CHARMM27 is built into the Gromacs 4.5.x
series, and CHARMM36 is available from the User Contributions section of the
website.
-Justin
Thank you for your help,
James
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
