[gmx-users] Simulation of membrane protein
jmsstarlight at gmail.com
Mon Oct 31 17:00:01 CET 2011
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 water topology
; Include ion topologies
; System specifications
[ system ]
128-Lipid DMPC Bilayer in water
[ molecules ]
; molecule name nr.
Also I've tried to make posre for whole system ( large posres ) but it also
was finished with same 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
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?
2011/10/31 Justin A. Lemkul <jalemkul at 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
>> 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 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users