[AMBER] missing bond parameter for Mg ion

From: Chen, Wei <weichen9.illinois.edu>
Date: Mon, 29 Jul 2019 21:35:22 +0000


I am trying to set up simulations for KRAS (using PDB id: 5vq2) with tleap. Since the protein comes with Mg ion and GTP, I used the force field for Mg and GTP from this website: http://research.bmh.manchester.ac.uk/bryce/amber. But I got the following error message:

/home/kengyangyao/.anaconda2/envs/py36/bin/teLeap: Error!
Could not find bond parameter for: CT - MG
Building angle parameters.

/home/kengyangyao/.anaconda2/envs/py36/bin/teLeap: Error!
Could not find angle parameter: OH - CT - MG

/home/kengyangyao/.anaconda2/envs/py36/bin/teLeap: Error!
Could not find angle parameter: H1 - CT - MG

/home/kengyangyao/.anaconda2/envs/py36/bin/teLeap: Error!
Could not find angle parameter: CT - CT - MG

/home/kengyangyao/.anaconda2/envs/py36/bin/teLeap: Error!
Could not find angle parameter: CT - CT - MG
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <gtp 170>: C8 C4 N9 C1'
 <gtp 170>: C5 N1 C6 O6
 <gtp 170>: C6 C2 N1 H1
 <gtp 170>: C2 H21 N2 H22
 <gtp 170>: N7 N9 C8 H8
 <gtp 170>: N1 N3 C2 N2
 total 543 improper torsions applied
 6 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.

/home/kengyangyao/.anaconda2/envs/py36/bin/teLeap: Warning!
Parameter file was not saved.

Exiting LEaP: Errors = 5; Warnings = 2; Notes = 1.

I checked the pdb file, it does not seem to contain atom "CT" so I am a bit confused about the error message, and wonder if anyone have idea what the issue may be and how I could fix it?

Thank you!

Best Regards
Wei Chen

Physics, UIUC
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Received on Mon Jul 29 2019 - 15:00:02 PDT
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