VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Mon Aug 11 2014 - 21:09:34 CDT

Oops, looks like I may have misinterpreted your question. If your problem
is, as Tristan suggests, an issue of having an unaligned map and structure
then you indeed need to do an initial docking either manually or with a
tool like Situs as the tutorial suggests.

On Mon, Aug 11, 2014 at 8:13 PM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:

> Personally, I’d do it the other way around. Desolvate your structure,
> fit it into the map (either by moving it manually in VMD or using a package
> like Situs), save your coordinates, re-solvate and go from there.
>
>
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Luba Simhaev
> *Sent:* Monday, 11 August 2014 7:23 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: MDFF simulations
>
>
>
> Hello,
>
>
>
> I would like to know how can I fit the target density map into the
> simulated box in a case that they are rotated with respect to each other?
>
>
>
> I saw in the tutorial that it's not supported by VMD. Maybe there is
> another way?
>
>
>
> Thanks!
>
>
>
> Regards,
>
> Luba
>