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TinkerTools / poltype2

Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA
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Spatial::LSTCAP #39

Closed mayank-kohli closed 8 months ago

mayank-kohli commented 8 months ago

Hi,

I am stuck at few places

  1. I am getting the following error:

GPU Device : Setting Device ID to 0 from GPU utilization Backtrace 1 analyze9 0x17c64d 2 analyze9 0x164a54 3 analyze9 0x15c5a9 4 analyze9 0x18ca77 5 analyze9 0x19014f 6 analyze9 0x1915c4 7 analyze9 0x20f8d 8 /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main 9 analyze9 0x21ebe Terminating with uncaught exception : An internal array in Spatial requested 12994 elements, but only 7968 (48166) were allocated. Please increase Spatial::LSTCAP (current value 48) so as to make Spatial::LSTCAP166 >= 12994.

  1. I have Zinc ion in my system, but in uncomplexed.pdb there is no zinc ion

  2. The complex_receptoronly.pdb is looking like this: image

leucinw commented 8 months ago

It seems that the 1st error is about Tinker9, not Poltype. I suggest you report to Tinker9 For the 2 and 3, I am not sure what are the issues. Do they relate to Poltype?

mayank-kohli commented 8 months ago

the issue 3 is happening after the complex formation, which I guess is leading to issue number 1 and the protein has a zinc ion but it not showing in any of the output.

leucinw commented 8 months ago

If you are using poltype to generate the simulation box, I suggest you use other tools, such as xyzedit.x in Tinker or CHARMM-GUI box generator. We want to limit poltype's function to small molecule parameter generator for AMOEBA and AMOEBA+ models. Other functions have not been extensively tested and will be removed in the future.

mayank-kohli commented 8 months ago

oh okay, I ll generate with the suggested tools.

Thank you