Hi,
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.
Quit
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
