[gmx-users] Doubts in visualisation of sdf output

Justin Lemkul jalemkul at vt.edu
Mon Jun 4 14:03:32 CEST 2018

On 6/4/18 7:05 AM, Apramita Chand wrote:
> 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.

You want the opposite of that - solvent for SDF and peptide for 
coordinate output.


> 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,
> Apramita


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list