[gmx-users] backmapping protein + dppc

[Adriana Garro]

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)
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
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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