[gmx-users] backmapping protein + dppc
Adriana Garro
adrianagarrosl at gmail.com
Wed Jan 28 17:53:07 CET 2015
Hi Tsjerk,
Don't worry, I just did the changes you suggested and now it works!
Thanks very much!
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
**********************************************************
2015-01-28 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.
> > > >>> --
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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.
> --
> Gromacs Users mailing list
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