[gmx-users] Re: Preparation of the pure lipid system with charmm force field
Mark.Abraham at anu.edu.au
Fri Oct 21 08:53:05 CEST 2011
On 21/10/2011 5:41 PM, James Starlight wrote:
> I've also tried to make topology for my system parametriesed for
> charmm36 ff by hands but failed too :(
> This is my topology for the POPC bilayer wich I've made in VMD
> membrane builder as well as downloaded a pre built membrane system (
> I've tested for both cases)
> ; Include chain topologies
> #include "charmm36.ff/forcefield.itp"
> ; Include lipids
> #include "charmm36.ff/lipids.rtp"
.rtp files may not be #included
> ; Include water topology
> #include "/charmm36.ff/tip3p.itp"
Initial backslash refers to the root of your file system, so is likely
> ; Include ion topologies
> #include "charmm36.ff/ions.itp"
> ; System specifications
> [ system ]
> 128-Lipid POPC Bilayer in water
> [ molecules ]
> POPC 72
> When I've loaded my molecule to grompp I've obtained error
> Program grompp, VERSION 4.5.4
> Source code file: /tmp/gromacs-4.5.4/src/kernel/toppush.c, line: 770
> Fatal error:
> Unknown bond_atomtype 1
> What does it means? Is here anybody who also tried to parametriesed
> theis lipids by charmm ff ?
Don't blame the ff yet :-)
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