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bioexcel / biobb_chemistry

Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.
https://mmb.irbbarcelona.org/biobb/
Apache License 2.0
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ambertools.reduce_add_hydrogens #4

Closed etweisberg closed 2 years ago

etweisberg commented 2 years ago

There is currently no parameter for bumping, which are part of the native AmberTools reduce program and are necessary sometimes for hydrogens that are skipped due to being too close to other atoms and short bond lengths (as suggested by the warning message in the standard output).

It would be super helpful if this functionality could be added to this wrapper.

etweisberg commented 2 years ago

Example of output warning message from reduce program:

WARNING: A 221 PL3 O1   H atom too close to  A 221 PL3 C1   by 0.011267A
        you may need to adjust using -METALBump or -NONMETALBump.
gbayarri commented 2 years ago

Hi,

We will add in the new release.

Thanks!

gbayarri commented 2 years ago

Implemented at:

https://github.com/bioexcel/biobb_chemistry/blob/master/biobb_chemistry/ambertools/reduce_add_hydrogens.py

It will be added to the new release.