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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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 03 2015 - 13:00:04 PST
