Dear Amber Users,
I will be running an entropy calculation using normal modes. As I
understood from Genheden et al. 2012, truncated systems are more efficient
than using the full system. I have a couple of questions regarding the
methodology.
1) I'll use cpptraj to truncate both the trajectories and the topology
files based on distance-dependent residue masks. Is this right or should I
use tleap?
2) Do I have to somehow "cap" the exposed bonds that will occur after
truncation?
3) The reference mentioned that all residues beyond 8 A were kept fixed
during the minimization and frequency calculations. How o I achieve that?
Is there a certain option in the input files that allow for fixing residues
based on names or distance? Please help with this.
Thanks in advance.
--
Ahmed Taha Ayoub
PhD Student, Theoretical and Computational Chemistry
W4-54, Department of Chemistry
11227 Saskatchewan Drive
University of Alberta
Edmonton, Alberta T6G 2G2
Canada
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Received on Wed Apr 02 2014 - 12:00:03 PDT
