[gmx-users] Preparation of the pure lipid system with charmm force field

James Starlight jmsstarlight at gmail.com
Thu Oct 20 14:56:14 CEST 2011

Dear, Gromac's users!

Today I've tried to make pure lipid bi-layer system from initial .pdb
structure with the parametrization by the charmm ff. The main goal of this
step is preparing the initial structure suitable for the futher simulation (
creating gro, top and posre files)

First I've download s system consisted of 72 dppc lipids solved with water.
Then I've succesfull created .gro as well as .top files by the pdb2grmx for
my lipid system.
But on futher during creatinon of the tpr file by gromp I've obtained many
errors like this

ERROR 4378 [file topol.top, line 83773]:
  No default U-B types

Also I've tried to make my own bi-layer by VMD membrane plugin. After
processing of this file by pdb2gmx I've obtained many .itp files like
topol_Other_chain_L2.itp included in the generated topology file topol.top.

But during loading this structure to the grompp I've obtained above
mentioned error again. In both cases I've used mdp file for gromp consist of
minimization algorithm ( attached).

What I've done wrong? Could you provide me with the workable algorithm for
preparation of the pure lipid system parametriezed by charm27 ?

Finally I have small queation about charmm structures- I've found already
pre-equilibrated bi-layers
http://terpconnect.umd.edu/~jbklauda/research/download.html where each pdb
file is accompanied by the PSF ones. As I've understood the PSF is the same
to the top in the Gromacs. Could I convert PSF to the TOP for already
pre-built system?

Thanks for help

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