VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Mon Mar 12 2018 - 11:35:40 CDT

Is there a reason you can't just change the chain ID of the conflicting
chains so they remain unique?

On Mon, Mar 12, 2018 at 10:15 AM Rune Thomas Kidmose <rtk_at_mbg.au.dk> wrote:

> Hi,
>
>
> Basically I would like to know, if it is possible to run a MDFF
> simulation on a whole 70S ribosome at once?
>
>
> I have only been able to do it on the LSU and then on the SSU separately,
> due to the constraints of the PDB format regarding unique chain ID's.
> Afterwards I then combine the two trajectories for visualization purposes
> only.
>
>
> Obviously the way I do it, the LSU does not feel or know anything about
> the SSU and vice versa.
>
>
> But I was wondering if it is possible to supply MDFF with multiple PSF
> and PDB files and multiple gridpdb files as well, but only one
> gridmap, which could then enable running MDFF on a whole ribosome at once.
>
>
> I have played around a bit with it, but I have not been able to make
> MDFF accept multiple PSF and PDB files.
>
>
>
> Cheers
>
>
> Ruki
>
>
>
>
>
>
>