Hi Yikan,
Below is a simple python script that should do it.
Best,
Guillermo
# Read PSF file.
import protocol
protocol.initStruct('yourpsffile.psf') # for examples on how to generate this
file see: eginput/PSF_generation
# Load parameters (bond lengths, angles, etc.).
protocol.initParams('protein.par')
# Load input structure.
protocol.initCoords('yourstructure.pdb')
# Correct covalent geometry.
protocol.fixupCovalentGeom()
# Write coordinates.
import pdbTool
pdbTool.PDBTool('newstructure.pdb').write()
________________________________________
From: ZhangYikan [[email protected]]
Sent: Friday, June 24, 2016 8:15 AM
To: [email protected]
Subject: [Xplor-nih] fix the molecular covalent geometry
hello all:
I want to generate a conformation pool for my RNA, so I used the EINemo to
generate my perturbed structure.
however, in my large bundle of pdb files from the EINemo, there are some
violation in the geometry of bonds.
Are there some useful tools(or tutorial) to fix my violation in the xplor-NIH?
Best wishes
Yikan
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