Hi Jasmin,
May I kindly know which version of MCPB.py you are using? In AMBER24, the MCPB.py automatically uses "source leaprc.water.opc", instead of "source leaprc.water.tip3p" in step 4 while generating the tLEaP file.
This might be the source but I am not 100% sure with the current information. Thank you for revealing more details (like what if you tried OPC instead of TIP3P in your system etc.) Thank you!
Best regards,
Zhen.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Jasmin Güven via AMBER <amber.ambermd.org>
Sent: Wednesday, June 11, 2025 10:44 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] TIP3P Water issue with MCPB.py
Hi All,
I’ve been trying to parameterise a metalloenzyme using MCPB.py.
I’ve successfully carried out the DFT calculations for the bonded terms and the partial charges using RESP.
However, when I run tleap, I get an error stating that the H1-Y4-H2 angle is not defined. Y4 is my water oxygen as defined by MCPB.py.
I took a look at the ZAFF.frcmod file and noticed that the HW-O1-HW angle is defined with a force constant of 100 and an angle of 104.5 degrees. I’ve manually added this line to my MCPB.py-generated frcmod file and this seems to have fixed the issue.
I wanted to ask if this might be a bug in the MCPB.py code and if so, could the angle be added automatically?
Many thanks in advance,
J. Jasmin Güven (she/her) AFHEA
.jjguven
Room 234
School of Chemistry
University of Edinburgh
David Brewster road
Edinburgh, EH9 3FJ
United Kingdom
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Received on Wed Jun 11 2025 - 11:30:02 PDT
