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

James Starlight jmsstarlight at gmail.com
Fri Oct 21 08:41:15 CEST 2011

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"

; Include water topology
#include "/charmm36.ff/tip3p.itp"

; Include ion topologies
#include "charmm36.ff/ions.itp"

; System specifications
[ system ]
128-Lipid POPC Bilayer in water

[ molecules ]

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 ?


2011/10/20 James Starlight <jmsstarlight at gmail.com>

> 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
> James
> James
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