[gmx-users] Simulation of membrane protein
Mark.Abraham at anu.edu.au
Thu Nov 3 14:39:36 CET 2011
On 3/11/2011 9:32 PM, James Starlight wrote:
> 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
> 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
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
> 2011/11/2 Mark Abraham <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>
> On 02/11/11, *James Starlight *<jmsstarlight at gmail.com
> <mailto:jmsstarlight at gmail.com>> wrote:
>> Justin, Mark,
>> 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"
>> 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.
>> 2011/10/31 Justin A. Lemkul <jalemkul at vt.edu
>> <mailto: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 "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:
>> 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 <http://vt.edu/> | (540) 231-9080
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