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

[Justin A. Lemkul]

James Starlight wrote:
> I've excluded   "charmm36.ff/lipids.rtp" from my topology and obtain new 
> error
> Fatal error:
> 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 here
> 

I presented the details of this procedure to you already:

http://lists.gromacs.org/pipermail/gmx-users/2011-October/065311.html

-Justin

> 
> James
> 
> 
> 2011/10/21 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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 wrong.
> 
> 
> 
>         ; 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 :-)
> 
>     Mark
>     -- 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================