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I have a substrate that has a Br-C bond. In CHARRM the line below is included in the .str file:

LONEPAIR COLI LP1 BR C9 DIST 1.8900 SCAL 0.0

I have also included coordinates for the lone pair in the .pdb file:

ATOM 67 LP1 LIG 1 0.871 -0.147 -3.939 1.00 0.00 SUB

I was able to solvate, minimize, and run dynamics on the system. However, the lone pair does not move with the substrate, and the coordinates are not updated afterwards. This results in the lone pair being 4.5+ Å away from the bromine.

My question is if this is normal, or is there something additional I need to include? Please let me know if any additional details would be useful. Thanks in advance!

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  • $\begingroup$ Which MD software are you using? Is it CHARMM or is it something else? From the question it's not clear if you referring to just the forcefield or the software as well. $\endgroup$
    – S R Maiti
    Feb 19 at 23:02
  • $\begingroup$ I am using CHARMM for MD as well $\endgroup$ Feb 19 at 23:41
  • $\begingroup$ Sorry, I haven't used CHRAMM before, other people in the site can probably help. $\endgroup$
    – S R Maiti
    Feb 20 at 10:20
  • $\begingroup$ I don't know if it would help, but you may need to include more of the .str file. I haven't used CHARMM, but it looks like there are a number of options for specifying lone pairs. Do you have any better luck with one of these other options? $\endgroup$
    – Tyberius
    Jun 24 at 14:20
  • $\begingroup$ Check if your PSF file contains "NUMLPH" section. If not, maybe you have built the system and added LONEPAIR in the topology file later. In this case, you may need to setup LONEPAIR in the CHARMM input (using LONEPAIR command) and write out to PSF file again. $\endgroup$
    – Sunhwan Jo
    Aug 20 at 6:00