On 1/11/2011 3:00 AM, 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
The text of the error is exactly right about what is wrong. Please read
and take time to understand before firing off email. You will learn more
and faster if you read and understand documentation relevant to a
situation before asking questions, and you will use less of everyone
else's volunteer time. Also, if you follow that link, you will find a
worked example of fixing your problem.
What's most true for such multy system. Generate posre only for 1 part
or for whole system?
It is often more profitable to understand why the error occurs, rather
than guess at the form of the solution.
Mark
James
2011/10/31 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
James Starlight wrote:
Thanks, Justin
I'll test your program soon.
Today also I have some problems with generation of the posre
for lipids
I have lipid bilayer in pdb. Then I selected one lipid
molecule and move it to separate pdb and convert it to gro
via editconf.
Than I've used genres and generate posre file for 1 lipid.
Than I include tis posre to topology of my bilayer
using gropt I obtain eror that I'm using wrong posre topology
Also I've tried to include posre.itp to my lipid.itp ( this
file contain link to posre on default) This run didnt produce
any errors but as the result posres have not been worked ( I
obtained perturbed bilayer after minimization)
How I can generate work posre for my bilayer to prevent
perturbation after equilibration or minimization ?
Since posre.itp is the default name given to the protein position
restraint file by pdb2gmx, the first step is to use a different
name. Then, you have to add the new #include statement in the
correct location in the topology. Presuming you do that, the
lipids should be restrained in whatever manner you've specified.
-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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