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.
>
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>
>
--
Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
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Received on Fri Apr 17 2015 - 01:00:02 PDT
