Re: [AMBER] Transform TIP3P to OPC

From: He, Amy via AMBER <amber.ambermd.org>
Date: Sun, 9 Jun 2024 02:24:11 +0000

Hi!

OPC water has a slightly different geometry than TIP3P water. If you can tolerate the difference or are able to re-optimize water’s geometry in Terachem, you could just replace the atoms’ names and residues’ names in the PDB file (and delete the 4th point in OPC waters).

From: Abdelrahman, Noureen via AMBER <amber.ambermd.org>
Date: Saturday, June 8, 2024 at 6:19 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Transform TIP3P to OPC
Hello all,

Is there a way I can transform opc water atoms to tip3p? I am trying to use Terachem on a system, and I want to include water molecules in my QM region, but Terachem doesn't work with OPC. So I am wondering if there's a way to transform those specific water molecules that I want to include into TIP3P for Terachem to run?

Thanks,
Noureen
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!0Wh7egs-UX8HSLiAshtRQOdLwJi9-ck1GMV7I7XB495QRyo1VHb60KuNA3qt3r6kR3E7LcrB6TK2SNLoAwXb9k5AuKg$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!0Wh7egs-UX8HSLiAshtRQOdLwJi9-ck1GMV7I7XB495QRyo1VHb60KuNA3qt3r6kR3E7LcrB6TK2SNLoAwXb9k5AuKg$>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 08 2024 - 19:30:02 PDT
Custom Search