Dear Amber users,
I used the force field parameter of Bryce group(
http://research.bmh.manchester.ac.uk/bryce/amber) to generate topology file for a protein-ATP complex. I saved the PREP and FRCMOD as atp.prep and frcmod.atp. Here is the tleap command:
source leaprc.protein.ff14SB
loadamberparams frcmod.atp
loadamberprep atp.prep
mol = loadpdb c-src-atp.pdb
saveamberparm mol c-src-atp.prmtop c-src-atp.inpcrd
And the leap reported the following error:
Error: Could not find bond parameter for: C - O3
Building angle parameters.
Error: Could not find angle parameter: O - C - O3
Error: Could not find angle parameter: C - O3 - P
Error: Could not find angle parameter: CX - C - O3
Building proper torsion parameters.
Error: ** No torsion terms for O-C-O3-P
Error: ** No torsion terms for C-O3-P-O3
Error: ** No torsion terms for C-O3-P-O3
Error: ** No torsion terms for C-O3-P-OS
Error: ** No torsion terms for CX-C-O3-P
Building improper torsion parameters.
old PREP-specified impropers:
<atp 522>: C8 C4 N9 C1*
<atp 522>: C6 H60 N6 H61
<atp 522>: N7 N9 C8 H80
<atp 522>: N1 N3 C2 H2
<atp 522>: C5 N1 C6 N6
total 849 improper torsions applied
5 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Warning: Parameter file was not saved.
The structure of ATP in my pdb file is exactly the same as that in PKA kinase (PDB 1ATP). I think I didn't use the force field parameter file correctly. Could you please tell me how to do with this? Thank you!
Best,
Yao Li
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Received on Wed Jul 10 2019 - 08:00:02 PDT
