Hello,
I'm trying to using MCPB.py to parameterize the metal binding site for a zinc binding protein. I am following the instructions in:
Advanced Tutorial 20 -
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php
Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program -
https://pubmed.ncbi.nlm.nih.gov/33125655/
I am trying to create topology and coordinate files of the full system now that the metal binding site has been parameterized:
$ tleap -s -f {system}_tleap.in > {system}_tleap.out
It seems when running the tleap.in file the vdw and other parameters for my ligand atoms coordinating the zinc ions is missing:
/home/ucsf/miniforge3/envs/AmberTools23/bin/teLeap: Error!
For atom (.R<LG1 232>.A<P1 1>) could not find vdW (or other) parameters for type (p5)
..
This continues for all atoms of the small molecule(s) coordinating the zinc ions in the metal binding site.
The tleap.in file was generated in the previous step of the tutorial:
$ MCPB.py -i {sysem}.in -s 4
Best,
Eric
_______________________________________
Eric Hantz
Postdoctoral Research Fellow - Renslo Lab
UCSF - Pharmaceutical Chemistry
Email: eric.hantz.ucsf.edu
Phone: 570-688-8720
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Received on Mon Mar 31 2025 - 15:30:02 PDT
