On 9/25/19 5:46 AM, Pandya, Akash wrote:
Hi,
I have multiple ligand molecules of the same type in my system. If I wanted to
monitor the Cartesian coordinates of each individual ligand during a
simulation, is there a Gromacs tool to do that? or do I have write a custom
script?
You can print coordinates over time using gmx traj.
-Justin
Some background:
My purpose is to look at binding/unbinding events for each ligand individually.
I have calculated the minimum distance between protein residues and ligands in
my system, but this does not give the identity of the ligand (e.g. resid or
atom number) within a particular cut-off. I used the gmx pairdist module in
Gromacs to calculate the minimum distance.
Any guidance will be much appreciated.
Best wishes,
Akash
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==
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129
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