From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Thu Oct 27 2016 - 06:13:10 CDT
Hi,
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
}
best
Abhi
Abhishek Tyagi
PhD Student
Chemical and Biomolecular Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Ma'Mon Hatmal <hatmal_at_usc.edu>
Sent: Thursday, October 27, 2016 6:22:52 PM
To: namd-l_at_ks.uiuc.edu
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.
Best,
-- 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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