Re: [AMBER] kindly guide me

From: Pietro Aronica <>
Date: Wed, 19 Feb 2020 19:43:27 +0800

PDBs generally do not have information about bonds (unless there are
CONECT records) and programs like VMD usually calculated bonds based on
proximity. Try saving it as a prmtop and inpcrd then visualise those,
and see if it draws a bond.

On 19/2/20 7:33 pm, ALAMGIR KHAN wrote:
> in xleap I run a bond command " bond 4HCU.442.SG 4HCU.619.C25", it ran okay, and save the pdb, while i checked in chimera, i observe that there is no bond between residue 442 and ligand C25 Atom.
> I don't know what happen there, kindly guide me, what could be reason behind this.Thank you
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Feb 19 2020 - 04:00:03 PST
Custom Search