Date: Wed, 11 Jun 2025 18:41:19 +0000
Hi Zhen,
Thanks for the quick reply!
I’m using AmberTools24 and I specify the water model as TIP3P and the protein FF as ff14SB in my mcpbpy.in file.
I wouldn’t like to use OPC as I’m using ff14SB and have been using it for other metal models. For more direct comparison I would like to keep the water and force fields as they are, if possible.
Just as an update, with this fix I managed to run a test minimisation, equilibration and a short MD simulation without problems.
Many thanks again,
Jasmin
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J. Jasmin Güven (she/her) AFHEA
.jjguven
Room 234
School of Chemistry
University of Edinburgh
David Brewster road
Edinburgh, EH9 3FJ
United Kingdom
https://mey-research.org<https://mey-research.org/>
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On 11 Jun 2025, at 19:25, Li, Zhen <lizhen6.chemistry.msu.edu> wrote:
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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<mailto:amber.ambermd.org>>
Sent: Wednesday, June 11, 2025 10:44 AM
To: amber.ambermd.org<mailto:amber.ambermd.org> <amber.ambermd.org<mailto: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
https://urldefense.com/v3/__https://mey-research.org__;!!HXCxUKc!0_t8NSmrbDVG1MdHynxDL3I7vRzIyCpfYFbS_IyCgHFuENpX4S_SXln1FcEefXZ2SobzXbJLe2QrB34HCHe9vmQ$
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