Date: Thu, 3 Dec 2015 23:39:04 -0500
I have attached a copy of the image that I get when I run the command
vmd -parm7 amber.top -rst7 amber.crd
You can clearly see some absurd bonds, which *are* defined in the prmtop
file (which is why they're rendered). When you visualize GRO or PDB files
with VMD, the bonds are drawn by distance so you don't these long bonds do
not seem to be present. But in the prmtop file they are, which is causing
your problem.
So this is your problem. You have to figure out where those came from and
prevent it from happening. ParmEd *did* actually convert the files to
GROMACS correctly, the problem was in your original Amber files.
HTH,
Jason
On Thu, Dec 3, 2015 at 11:28 PM, mohammad r <mohammad.r0325.yahoo.com>
wrote:
> The files are attached.
>
> Thank you, Mohammad.
>
>
>
> On Friday, December 4, 2015 1:07 AM, mohammad r <mohammad.r0325.yahoo.com>
> wrote:
>
>
> The files are attached.
>
> Thank you, Mohammad.
>
>
>
>
> On Friday, December 4, 2015 12:57 AM, mohammad r <mohammad.r0325.yahoo.com>
> wrote:
>
>
> The files are attached.
>
> Thank you, Mohammad.
>
>
>
> On Friday, December 4, 2015 12:29 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>
> Can you attach a compressed tarball of your prmtop and coordinate file so I
> can look at it?
>
> On Thu, Dec 3, 2015 at 2:27 PM, mohammad r <mohammad.r0325.yahoo.com>
> wrote:
>
> > I could open the amber crd and top files but I thinksomething is wrong
> > with it. In line and bond drawing method a line connectionis between my
> > system and a point in far away from my system. I attached theimage, my
> > system is located on the left hand and a line is out of it. But this line
> > does not appear
> >
> > in the gro file.
> >
> >
> > On Thursday, December 3, 2015 9:47 PM, Brian Radak <
> > brian.radak.accts.gmail.com> wrote:
> >
> >
> > I can't speak directly to the VMD internals, but my experience has led
> > me to believe that VMD will skip the heuristic distance check if a
> > topology file (e.g. PSF or prmtop) is read. This seemed most apparent to
> > me by looking at rigid waters or disulfide linkages with and w/o loading
> > a PDB with a matching PSF.
> >
> > Brian
> >
> > On 12/03/2015 12:05 PM, Jason Swails wrote:
> > > On Thu, Dec 3, 2015 at 12:55 PM, mohammad r <mohammad.r0325.yahoo.com>
> > > wrote:
> > >
> > >> When I open the amber topology file in vmd, it can read the number of
> > >> atoms but the number of frames is zero so it shows nothing, in opening
> > the
> > >> .crd file the number of frames and atoms are zero. But when I open the
> > .gro
> > >> file it shows the system correctly.
> > >>
> > > You need to load both the prmtop *and* the coordinate file. The
> prmtop
> > > defines the molecule, and the crd file provides the frame.
> > >
> > > Make sure you load the coordinate file as the correct type. If it is
> the
> > > inpcrd file, you need to select "Amber 7 restart", not "Amber
> > coordinates".
> > >
> > > As for the GRO file showing the system correctly -- I believe this is
> > > because VMD draws the bonds based on distance, NOT necessarily what is
> > > inside the Gromacs or Amber topology files. You really need to check
> the
> > > appearance of the Amber topology file with Amber coordinates to see if
> > some
> > > mistake was made there.
> > >
> > > HTH,
> > > Jason
> > >
> >
> > --
> > Brian Radak
> > Postdoctoral Scholar
> > Gordon Center for Integrative Science, W323A
> > Department of Biochemistry & Molecular Biology
> > University of Chicago
> > 929 E. 57th St.
> > Chicago, IL 60637-1454
> > Tel: 773/834-2812
> > email: radak.uchicago.edu
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
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> >
> >
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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>
>
>
>
>
>
>
-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher
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