Re: Problem with minimization

From: Abhishek TYAGI (
Date: Thu Oct 27 2016 - 06:13:10 CDT


Its easy, if you have followed the NAMD tutorial, they have mentioned about how to fix the Beta and occupancy in pdb file, then you can do it. In the namd config file then you have to write the following thing:

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile fixed.pdb
fixedAtomsCol B
fixedAtomsForces on



Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

From: <> on behalf of Ma'Mon Hatmal <>
Sent: Thursday, October 27, 2016 6:22:52 PM
Subject: namd-l: Problem with minimization

Hi Everyone,
I have a problem with minimization, I have a pdb file which contains enzyme (mTOR) and its ligand.
I need to do the minimization only for the ligand while fixing the enzyme.
If you can please help in that and what to do with the config file.


Dr. Ma'mon Hatmal
PhD and MSc in Biochemistry and Molecular Biology
MSc in Global Medicine
BSc in Medical Laboratory Sciences

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