Hi Alexander,
Sorry for the late reply. I do know why I missed/forgot the email...
I can not open your zip file… Have you figured out the problem?
-Pengfei
> On May 27, 2020, at 6:29 AM, Oleksandr Kravchenko <okr.kth.se> wrote:
>
> Hi!
>
>
> I would like to use Amber18 for the simulation of a ruthenium complex in water. Fir this, I need to parametrize the complex with a bonded model, which I am trying to do using MCPB.py. So far I have succesfully made it to the last step which is running tleap. However, some bond parameters are missing:
>
>
> /software/sse/manual/Amber/18/i17/bin/teLeap: Error!
> Could not find bond parameter for: ca - hc
>
> /software/sse/manual/Amber/18/i17/bin/teLeap: Error!
> Could not find bond parameter for: c3 - ha
>
> /software/sse/manual/Amber/18/i17/bin/teLeap: Error!
> Could not find bond parameter for: c3 - ha
>
> /software/sse/manual/Amber/18/i17/bin/teLeap: Error!
> Could not find bond parameter for: ca - hc
> Building angle parameters.
>
> /software/sse/manual/Amber/18/i17/bin/teLeap: Error!
> Could not find angle parameter: ca - ca - hc
>
> /software/sse/manual/Amber/18/i17/bin/teLeap: Error!
> Could not find angle parameter: ha - c3 - hc
>
> ... and some more angle parameters. The rest seems to proceed well, but this looks odd to me. I would expect that these [default] bond/angle parameters should exist in the force field (ff14SB as it is the default MCPB uses) as these are the common GAFF types. If you look closely, these are also bonds and angles that should not normally be bonded (like c3 and ha - aliphatic carbon and aromatic hydrogen).
>
> And there is another strange thing. In step 2 of MCPB new bond/angle parameters are built, namely several metal-ligand bonds (like M1-Y6) and angles that include at least two of new atom types (like M1-Y6-ca). However, in the tleap output I get these errors:
>
> /software/sse/manual/Amber/18/i17/bin/teLeap: Error!
> Could not find angle parameter: Y6 - ca - ha
>
> This angle does exist in the structure - but why does MCPB not add a parameter for it then? Hope for you competence to help! Files are attached for your reference.
>
> Best wishes,
> Alexander?
>
> <biqa_tleap.out><tleap_input_files.zip>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 20 2020 - 12:30:04 PDT
