From: Luba Simhaev (luba.simhaev0703_at_gmail.com)
Date: Tue Aug 12 2014 - 01:44:02 CDT

Thank you for your replies.
This is a little bit more complicated, since the simulated system contains
not only the water box but also a membrane. Which means that prior to MDFF
simulations I used the initial docked protein structure (to the denstiy
map) for placing it in a membrane (according to the membrane protein
tutorial in VMD). As a result the orientation of the protein system and the
density map are changed.

Thanks,
Luba

On Tue, Aug 12, 2014 at 5:09 AM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
wrote:

> 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
>>
>
>