[gmx-users] Simulation of membrane protein

[James Starlight]

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 )

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?

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?


Thank you for your help,

James
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