VMD-L Mailing List

From: Rune Thomas Kidmose (rtk_at_mbg.au.dk)
Date: Mon Mar 12 2018 - 11:49:41 CDT

That is something I have done when I for example was doing MDFF on spliceosomes etc.

There I had to make sure all chains were unique and when I ran out of chain IDs I had to reuse chain IDs making sure the resid’s were unique. So my normal procedure was to increment the resid with a value that ensured that no chains had the same residue number twice (or more).

So yes that is one way, but it takes time and it makes down stream analysis slow and more complex than needed. And I do have PDBs with to many atoms and chains to fit inside a PDB file, at least as long as I can’t use two character chain IDs.

Also I want something that works with a minimal of manual intervention, so if it was possible to run multiple PDBs at once I would strongly prefer that.

Cheers

Ruki

Den 12. mar. 2018 kl. 17.35 skrev Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu<mailto:ryanmcgreevy_at_ks.uiuc.edu>>:

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<mailto: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