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.abra...@anu.edu.au
<mailto:mark.abra...@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
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