[gmx-users] backmapping protein + dppc

Wed Jan 28 16:39:54 CET 2015

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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