Re: Issue with preparing QM-MM

From: Victor Kwan (
Date: Thu Feb 27 2020 - 16:26:39 CST

Hi Francesco,

In VMD: Load the last frame of your DCD and the modified pdb. File -> Save Coordinates -> First 0 Last 0, Save as a new pdb.

You'll get a pdb file with modified resid and the coordinate of the system after equilibrium. You might have to fix the O/B column afterward.

On Thu, Feb 27, 2020 at 5:03 PM Francesco Pietra <<>> wrote:
I Victor
setting up QM-MM needs a psf and a related pdb

On Thu, Feb 27, 2020 at 9:45 PM Victor Kwan <<>> wrote:
Hi Francesco,

DCD files does not contain topological information (resid, etc), only the atom number. It does not matter if you load a psf containing resid 0 or resid 999 after you load the dcd.


Kind regards,

Victor Kwan


On Thu, Feb 27, 2020 at 3:28 PM Francesco Pietra <<>> wrote:
Hello Victor, of course, as implied in my "renumbering". 3 ,5 etc are fictitious resid ID, which in reality were not in consecutive order. i am trying to save the MD work that i did with resid 0.

On Thu, Feb 27, 2020, 21:02 Victor Kwan <<>> wrote:
Hello Francesco,

ResID does not have to be in numerical order. I have attached a short proof of concept of 216 SWM4-NDP water that starts with resid 999. You can easily change the resid from 0 to 999 in your pdb and psf files.

Kind regards,


On Thu, Feb 27, 2020 at 1:40 PM Francesco Pietra <<>> wrote:

My question is whether there is a way to circumvent the inability of <prepare.qm.region.tcl> (vmd text mode) with nucleotides and a small organic ligand, to recognize residue number 0 for the organic ligand

set seltext "(nucleic and resid 0 3 5 7 8 9)"

the generated .QMonly.psf contains all except what relates to resid 0.
I understand that I could renumber the starting pdb and rebuild psf/pdb, but I have already equilibrated the system with resid 0. Segname is not useful here because it does not discriminate the nucleotides.

Thanks for advice
francesco pietra

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