[gmx-users] Doubts in visualisation of sdf output

[Justin Lemkul]

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.

-Justin

> 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

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

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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