Re: [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file.

From: Bill Ross <>
Date: Thu, 19 Oct 2017 12:06:43 -0700

The bond info is in the prmtop file, so with the pdb, unless the
visualization program recognizes residues on their own to figure out
what bonds to draw, you will not see bonds.


On 10/19/17 11:16 AM, Rana Rehan Khalid 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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Received on Thu Oct 19 2017 - 12:30:02 PDT
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