[gmx-users] backmapping protein + dppc
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Jan 28 17:33:46 CET 2015
Hi Adriana,
The order of atoms should be the same, I guess. So the easiest is to rename
the atoms in dppc.itp to match the ones in dppc.gromos.map. You can also do
the other way around, but then you have to be careful to rename throughout
the file (also in the modifiers).
I'm sorry about this. But it's not doable to manage all different naming
schemes for all force fields :S Well, maybe it is, but not in the way it's
implemented now.
Cheers,
Tsjerk
On Wed, Jan 28, 2015 at 5:10 PM, Adriana Garro <adrianagarrosl at gmail.com>
wrote:
> They don't :-(
> what can I do?
>
> Thanks
>
> ***********************************************************
> Dra. Adriana D. Garro
> Química Medicinal
> Facultad de Química, Bioquímica y Farmacia
> Universidad Nacional de San Luis
> IMASL-CONICET
> San Luis, Argentina
>
> Tel..............:+54 266 4424689 int 6153
> e-mail...: adgarro at unsl.edu.ar
> e-mail...: adrianagarrosl at gmail.com
>
>
> **********************************************************
>
> 2015-01-28 17:05 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>
> > Hi Adriana,
> >
> > Can you check if the names in dppc.itp match with those in
> dppc.gromos.map
> > in the Mapping directory of backward?
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Wed, Jan 28, 2015 at 4:39 PM, Adriana Garro <adrianagarrosl at gmail.com
> >
> > wrote:
> >
> > > Hi Tsjerk
> > >
> > > I am still dealing with the backmap of my protein DPPC system.
> > > Today I am pretty sure that the problem is not the force field
> > > (gromos53a6_lipid.ff/) because it is the one I built following the
> KALP
> > > tutorial and it worked when I run pdb2gmx on a protein+dppc system. So
> I
> > > think if it works in this sense would be the same in order to do the
> > > backmap because the system is almost the same (I have a different
> protein
> > > of course).
> > > I use this command line
> > >
> > > /initram.sh -f reimaged_coord.gro -o aa_gromos53a6.gro -to gromos53a6
> -p
> > > topol.top
> > >
> > > and the error message
> > >
> > > Fatal error:
> > > number of coordinates in coordinate file (0-backward.gro, 21006)
> > > does not match topology (backmapped.top, 28806)
> > >
> > > so I visualize with vmd my system 0-backward.gro
> > > and the DPPS lipids are missing!
> > >
> > > while, backmapped.top
> > > DPPC 156
> > > SOL 6888
> > > CL 8
> > >
> > > that is the difference between these 2 files.
> > >
> > > I did something different just to try
> > > I commented DPPC in the atomistic topol.top file and again
> > >
> > > /initram.sh -f reimaged_coord.gro -o aa_gromos53a6.gro -to gromos53a6
> -p
> > > topol.top
> > >
> > > and the error message is different this time
> > >
> > > Fatal error
> > > number of coordinates in coordinate file (0-backward.gro, 28806)
> > > does not match topology (backmapped.top, 21006)
> > >
> > > You see, the numbers are interchanged.
> > > Now 0-backward.gro has the DPPC lipids (and they look ok) but of course
> > due
> > > to these files do not agree the operation fails.
> > >
> > > Maybe with your experience you can realize what is happening.
> > > Thanks for your help!
> > >
> > > Adriana
> > >
> > >
> > >
> >
> ---------------------------------------------------------------------------------------------------------------------
> > >
> > > 5-01-27 18:29 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> > >
> > > > Hey :)
> > > >
> > > > Right. The backmapping uses the atomistic topology, just like any MD
> > > based
> > > > protocol (well, and in another way too, but that's not relevant
> here).
> > > The
> > > > Tieleman lipids are not compatible with G53a6 just like that. You
> > should
> > > be
> > > > able to find lipids for that FF from David Poger.
> > > >
> > > > Justin, it's sure worth trying once ;)
> > > >
> > > > Cheers,
> > > >
> > > > Tsjerk
> > > > On Jan 27, 2015 6:20 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 1/27/15 8:55 AM, Adriana Garro wrote:
> > > > >
> > > > >> Hi Tsjerk,
> > > > >>
> > > > >> Yes, you are right, it was :-)
> > > > >> But now a have a new error message
> > > > >>
> > > > >> Atomtype LC3 not found
> > > > >>
> > > > >> I have in the working directory:
> > > > >> dppc.itp (Dr. Tieleman website)
> > > > >> lipid.itp (Dr. Tieleman website)
> > > > >> gromos53a6_lipid.ff/ folder (with all the files modified according
> > to
> > > > >> kalp-15 tutorial)
> > > > >>
> > > > >
> > > > > I don't know anything about these back-mapping protocols between CG
> > and
> > > > > AA, but if you're getting an error related to an atom type not
> being
> > > > found,
> > > > > that means you haven't fully constructed the force field correctly.
> > > That
> > > > > error is usually triggered when the atom type in question is not
> > > present
> > > > in
> > > > > ffnonbonded.itp.
> > > > >
> > > > > -Justin
> > > > >
> > > > > topol-gromos53a6_lipid.ff.top
> > > > >> with
> > > > >> #include "gromos53a6_lipid.ff/forcefield.itp"
> > > > >> ; Include DPPC chain topology
> > > > >> #include "dppc.itp"
> > > > >> located in the correct place
> > > > >>
> > > > >> to prepare the atomistic topology I just used
> > > > >>
> > > > >> pdb2gmx -f protein-aa.pdb -ignh
> > > > >> then selected
> > > > >> gromos96-53A6
> > > > >>
> > > > >> Just the protein is in this file protein-aa.pdb (without lipids)
> > > > >> but then I edited the topology file adding the correct amount of
> > DPPC
> > > in
> > > > >> agreement with the CG coordinates file, water and iones seem not
> be
> > so
> > > > >> important here.
> > > > >>
> > > > >> Thanks for the help provided!
> > > > >> Cheers,
> > > > >>
> > > > >> Adriana
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >> ***********************************************************
> > > > >> Dra. Adriana D. Garro
> > > > >> Química Medicinal
> > > > >> Facultad de Química, Bioquímica y Farmacia
> > > > >> Universidad Nacional de San Luis
> > > > >> IMASL-CONICET
> > > > >> San Luis, Argentina
> > > > >>
> > > > >> Tel..............:+54 266 4424689 int 6153
> > > > >> e-mail...: adgarro at unsl.edu.ar
> > > > >> e-mail...: adrianagarrosl at gmail.com
> > > > >>
> > > > >>
> > > > >> **********************************************************
> > > > >>
> > > > >> 2015-01-27 11:50 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> > > > >>
> > > > >> Hi Adriana,
> > > > >>>
> > > > >>> The message says #include"gromos...
> > > > >>> I guess you meant to have a space between them.
> > > > >>>
> > > > >>> Cheers,
> > > > >>>
> > > > >>> Tsjerk
> > > > >>>
> > > > >>> On Tue, Jan 27, 2015 at 11:31 AM, Adriana Garro <
> > > > >>> adrianagarrosl at gmail.com>
> > > > >>> wrote:
> > > > >>>
> > > > >>> Dear gromacs users,
> > > > >>>>
> > > > >>>> I am trying to backmap my system which is protein + dppc lipids.
> > > > >>>> I built the atomistic topology file according to the KALP-15
> > > tutorial
> > > > >>>> created by Justin Lemkul.
> > > > >>>> I have in my working directory a folder called
> gromos53a6_lipid.ff
> > > > with
> > > > >>>>
> > > > >>> all
> > > > >>>
> > > > >>>> the files modified in line with the tutorial.
> > > > >>>> Then I used this command line
> > > > >>>>
> > > > >>>> ./initram.sh -f reimaged_coord.gro -o aa_gromos96-53A6.gro -to
> > > > >>>>
> > > > >>> gromos53a6
> > > > >>>
> > > > >>>> -p topol-gromos53a6_lipid.ff.top
> > > > >>>>
> > > > >>>> and after several steps I have the following error message
> > > > >>>>
> > > > >>>> Program grompp, VERSION 4.6.3
> > > > >>>> Source code file: /usr/local/gromacs-4.6.3/src/kernel/topio.c,
> > line:
> > > > >>>> 640
> > > > >>>>
> > > > >>>> Fatal error:
> > > > >>>> Syntax error - File backmapped.top, line 20
> > > > >>>> Last line read:
> > > > >>>> '#include"gromos53a6_lipid.ff/forcefield.itp"'
> > > > >>>>
> > > > >>>> I would really appreciate some advices in order to solve this.
> > > > >>>> Thanks in advance!
> > > > >>>>
> > > > >>>> Adriana
> > > > >>>> --
> > > > >>>> Gromacs Users mailing list
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> > > > >>>
> > > > >>>
> > > > >>> --
> > > > >>> Tsjerk A. Wassenaar, Ph.D.
> > > > >>> --
> > > > >>> Gromacs Users mailing list
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> > > > >>>
> > > > >>>
> > > > > --
> > > > > ==================================================
> > > > >
> > > > > Justin A. Lemkul, Ph.D.
> > > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > > >
> > > > > Department of Pharmaceutical Sciences
> > > > > School of Pharmacy
> > > > > Health Sciences Facility II, Room 629
> > > > > University of Maryland, Baltimore
> > > > > 20 Penn St.
> > > > > Baltimore, MD 21201
> > > > >
> > > > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > > > http://mackerell.umaryland.edu/~jalemkul
> > > > >
> > > > > ==================================================
> > > > > --
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> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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Tsjerk A. Wassenaar, Ph.D.
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