[gmx-users] Re: Preparation of the pure lipid system with charmm force field
jmsstarlight at gmail.com
Fri Oct 21 12:47:46 CEST 2011
I've excluded "charmm36.ff/lipids.rtp" from my topology and obtain new
No such moleculetype POPC
How I could include topology on this lipids ( all of them are present in the
lipids.rtp. ) ?
I have itp for the lipids only for the GROMOS ff so it should not be used
2011/10/21 Mark Abraham <Mark.Abraham at anu.edu.au>
> 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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