[gmx-users] Doubts in visualisation of sdf output

Apramita Chand apramita.chand at gmail.com
Mon Jun 4 13:05:16 CEST 2018

Dear All,
I want the SDF of urea as well as water molecules around my peptide
molecule. For this purpose , I used trjconv to get traj1.xtc with -fit
rot+trans option(selecting peptide as fitting option and system as output).
Using this traj1.xtc, I generated traj2.xtc with centering the peptide and
again system as output.
On this traj2.xtc, I used g_spatial where I selected Peptide molecule for
SDF and then water molecules to output coordinates.
The grid.cube files for water and also urea have been formed.
However, how do I visualise the peptide molecule along with the isosurface?
Should I load a separate file containing only centered peptide coordinates?
Should that be .gro file for the entire trajectory?

Please advise.

Yours sincerely,

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