Hi,
On Thu, Sep 29, 2016 at 7:45 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> Hi,
>
> I have a protein-ligand complex in truncated octahedran box. I did minor
> modifications (deleted two atoms) in the system and want to start a new
> simulation using the old waterbox information.
>
> I tried to use setbox as follows:
> set var box {85.030 85.030 85.030}
>
> however, when i started the new simulation, I found the waterbox changed
> into "square" .
>
> then I changed IFBOX pointer in the prmtop file from 1--> 2.
>
> Now the trajectory looks fine.
>
> Is there any thing else which I need to take care?
I'm not sure, but I would be cautious. As you have found out, the
'setbox' command only works for orthogonal boxes. Manually setting the
box can be tricky and can sometimes lead to the simulation blowing up
due to imaging errors. If you were able to run simulations with this
modified topology with no issue it could be fine. The only other thing
I can think of is modifying BOX_DIMENSIONS in the topology so the
first number (beta) is 1.09471219E+02 instead of 9.00000000E+01. I
don't think any programs in Amber actually use that information but I
could be wrong...
-Dan
>
> Thanks,
> Hirdesh
> **
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 29 2016 - 07:00:02 PDT
