[gmx-users] Simulation of membrane protein
jmsstarlight at gmail.com
Wed Nov 2 10:00:29 CET 2011
not I've included posre only to the lipid.itp wich consist of parameters
for just 1 lipid
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 ?
2011/10/31 Justin A. Lemkul <jalemkul at 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"
>> ; 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
>> 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
>> website at http://www.gromacs.org/**Documentation/Errors<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:
> 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 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
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