Thanks you.
Regards
On Oct 19, 2017 11:19 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
> load the prmtop before loading the coordinates. When loading a pdb file,
> VMD uses distances. You should load the prmtop first if you want the bond
> information to come from Amber.
>
> On Thu, Oct 19, 2017 at 2:16 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
> > Hi Everybody
> >
> > I saved one frame of my simulation in the pdb file. But when I open this
> > pdb file in the vmd, chimera and in pymol it does not show the bond
> between
> > Histidine and iron while in the .mdcrd file which i loaded after .prmtop
> > file shows all the heme pyrole bond and coordinate bond between histidine
> > and Fe. Similarly the bond between Fe and NO also can be seen in the
> > trajectory file but after saving the frame in to pdb it vanished. can
> you
> > please guide me how i can visualized the bond in vmd.
> > Here is the attached images 1st one is the captured during md run in this
> > image all bond shows
> >
> > in the 2nd image is the pdb saved, one frame which i opened in chimera.
> >
> > Regards
> >
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> >
> >
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Received on Thu Oct 19 2017 - 11:30:05 PDT
