Carla Jamous wrote:
Hi everyone,
please is there a way to know if electrostatic interactions exist
between my ligand and my protein during the trajectory? Which tool can I
use for this purpose, other than g_saltbr?
You can quantify short-range nonbonded energies using energygrps, which at this
point would require using the -rerun feature of mdrun. You can also get a list
of contacts using g_mindist and/or g_dist, as well as distance matrices with
g_mdmat.
-Justin
Thank you,
Carla
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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