[AMBER] Bad atom type error and invalid periodicity error in MMPBSA.py

From: Yi Ren <yi.ren6.unsw.edu.au>
Date: Mon, 17 Jan 2022 08:13:37 +0000

Hi Amber users

Hope this email finds you well

As shown in the subject, I encountered a problem while using MMPBSA.py to calculate mmgbsa and mmpbsa

My protein contains an organometallic complex (with cobalt iron), which the forcefield parameter was generated by using MCPB.py
The topology file was generated by xleap without issue, and run the MD simulation without issue.

However, the MMPBSA.py could not recognize the cobalt iron (atom type assigned M1) and indicate the bad atom type.
The amber version I'm using the is the AmberTools21 and Amber 20.

When I run my mmpbsa, the error message is the "Found an invalid periodicity in the prmtop file: 233"

May anyone could give some help in here? Much appreciated.

Yi Ren
PhD candidate UNSW

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Received on Mon Jan 17 2022 - 00:30:02 PST
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