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

From: Carlos Simmerling <>
Date: Thu, 19 Oct 2017 14:19:00 -0400

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 <>

> 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 - 11:30:04 PDT
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