On 3/11/2011 9:32 PM, James Starlight wrote:
Mark,
Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already
have had gromos lipid ff)
than I made pdb file for just 1 molecule of the dppc lipid consisted
of 50 atoms and generate for that new molecule lipid_posres.itp via
pdb2gmx
than I've included lipid_posre.itp to the dppc.itp at the end of file
where the reference for the posres_lipid was already existed as
POSRES_LIPID.
Your free use of "lipid_posres.itp", "lipid_posre.itp" and
"posres_lipid" in your sentences above make it seem like you might not
have been using a file name that matches your #include.
I've included in the minim.mdp
define= - DPOSRES_LIPID
There's an extra space in that line. There's a reason people want to see
actual input and output and contents of files. Stuff filtered through
your head is stuff that you might have made an extra mistake with.
than I've minimized my bilayer dppc.gro and checked by VMD if the
bilayer was perturbed after simulation
So althought posres were included in the minim.pdb the bilayer was
perturbed ( tails of lipids were less ordered in comprison to the
initial bilayer )
Sounds like Andreas has the right idea.
Why posres didnt work?
Position restraints aren't magic - they're only applied to specific
atoms. You need to choose which. The genrestr GROMACS tool may be your
friend here.
Mark
2011/11/2 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 02/11/11, *James Starlight *<jmsstarli...@gmail.com
<mailto:jmsstarli...@gmail.com>> wrote:
Justin, Mark,
Ok
not I've included posre only to the lipid.itp wich consist of
parameters for just 1 lipid
#ifdef POSRES_LIPID
#include "posre_lipid.itp"
#endif
to the minim.mdp I've included
define = -DPOSRES_LIPID ; position restrain the lipids
As the result I have not obtained any error in grompp but after
minimization my lipid bilayer was perturbed. I've used very
strong posres. Why it have not worked ?
We can't know, because we don't know what's in any files, nor why
you think the bilayer was perturbed. If you would like useful
help, you need to be exhaustive in your description of what you
have done, what you have observed and what you think about those.
It is easier for people who might volunteer free help to do
something else with their time than to ask follow-up questions
when few details were given originally.
Mark
2011/10/31 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>>
James Starlight wrote:
I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each
of 50 atoms )
I've included this in the topology of the bilayer
; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
; Include ion topologies
#include "gromos53a6_lipid.ff/ions.itp"
#ifdef POSRES_LIPID
#include "posre_lipid.itp"
#endif
; System specifications
[ system ]
128-Lipid DMPC Bilayer in water
[ molecules ]
; molecule name nr.
DPPC 64
SOL 1193
SOL 690
Also I've tried to make posre for whole system ( large
posres ) but it also was finished with same error
Fatal error:
[ file posre_lipid.itp, line 6 ]:
Atom index (2) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology
section "position_restraints"
in a part belonging to a different molecule than you
intended to.
In that case move the "position_restraints" section to
the right molecule.
For more information and tips for troubleshooting, please
check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
What's most true for such multy system. Generate posre
only for 1 part or for whole system?
Position restraints can only be applied on a [moleculetype]
basis. Thus, order matters a lot, and the whole system
cannot be restrained in one file. See the example here:
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
As it stands now, the topology you've shown tries to apply
lipid position restraints after the ions have been #included,
which makes no sense at all.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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