Dear Karl and Dan,
thank you a lot for your answer, I did it wrong as said! And it works
perfectly both information provided! Thanks!
I will use this format Dan, thank you for this advise.
Have a great day / night!
Pierre.
*Pierre BERTIN*
Bioinformatics and Biostatistics student (MSc),
University Paris-Sud XI, ORSAY.
2015-04-17 8:00 GMT-06:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> In addition, consider saving your trajectory in NetCDF format in your
> simulations from the start (use input flag ioutfm=1). NetCDF has
> higher precision, is less prone to errors, is faster to process, and
> VMD can correctly determine whether the trajectory has box info or not
> automatically.
>
> -Dan
>
> On Fri, Apr 17, 2015 at 1:32 AM, Karl Kirschner <k.n.kirschner.gmail.com>
> wrote:
> > Hello Pierre,
> >
> > I believe the problem is how you are reading in the coordinate file
> into
> > VMD. There are two ways to do this - with or without periodic box
> > information. When you are in VMD and are within the New Molecule submenu,
> > make sure you select the correct file type when loading the trajectory of
> > that type (i.e. AMBER Coordinates or AMBER Coordinates with Periodic
> Box).
> > (Know that you need to first load the corresponding topology.) Hopefully,
> > this will solve your problem. Alternatively, you can use cpptraj to
> process
> > your trajectory and save it in different formats.
> >
> > Cheers,
> > Karl
> >
> > On Fri, Apr 17, 2015 at 8:51 AM, Pierre Bertin <bertinp71.gmail.com>
> wrote:
> >
> >> Dear users,
> >>
> >> I am trying to simulate a carbon nanotube in water. There are lot's of
> >> papers, so I have the parameters for each field of .frcmod file. I have
> >> also generated prmtop and inpcrd file from leap, where I charged ff14SB,
> >> gaff and cnt.frcmod (from parmchk2 and then edited to correct some
> >> parameters to write papers found and accepted parameters).
> >>
> >> *The problem* : After the minimisation and heating (300K), when I
> visualize
> >> heat.mdcrd file all carbon atoms are missplaced in the box extremities
> and
> >> waters molecules take the carbon nanotube place... The carbon nanotube
> is
> >> deaaad!
> >>
> >> This kind of behavior is revelating a wrong force field, right? Do I
> have
> >> to edit a .lib file and charge it with loadOff in leap for the carbon
> >> nanotube molecule?
> >>
> >> Thank you a lot for your time and possible answers o ways to solve this
> >> problem!
> >>
> >>
> >> *Pierre BERTIN*
> >> Bioinformatics and Biostatistics student (MSc),
> >> University Paris-Sud XI, ORSAY.
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Karl. N. Kirschner, Ph.D.
> > Research Associate
> > Bonn-Rhein-Sieg University of Applied Sciences
> > Grantham-Allee 20, 54757 Sankt Augustin, Germany
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Fri Apr 17 2015 - 09:00:03 PDT
