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C++ Delphi versions do not seem to understand the radii.siz (default.siz) file used together with previous versions. The beauty (and shortcoming) of the old file was that it only assigned a single radius per element. This does not seem to work any longer.
adapt atom and residue names in this file to Amber topology
make this the default radii file of Delphi wrapper
This file is optimized to be used with a different charge set. Not sure though, whether it makes any sense physically to combine these radii with amber charges. Better would be to re-create this file from the Amber topology. Radii are not given in the leap prep library files. Instead, they may be fetched from AmberTools/src/pbsa/sa_driver.F90, at least this is what is claimed here: http://archive.ambermd.org/201610/0088.html
The text was updated successfully, but these errors were encountered:
C++ Delphi versions do not seem to understand the radii.siz (default.siz) file used together with previous versions. The beauty (and shortcoming) of the old file was that it only assigned a single radius per element. This does not seem to work any longer.
As a temporary workaround, I am adding the new "sample radius file" from the Delphi web site:
https://honiglab.c2b2.columbia.edu/software/DelPhi/doc/parseres.siz
biskit/data/delphi/radii_delphi_v7.siz
Delphi
wrapperThis file is optimized to be used with a different charge set. Not sure though, whether it makes any sense physically to combine these radii with amber charges. Better would be to re-create this file from the Amber topology. Radii are not given in the leap prep library files. Instead, they may be fetched from
AmberTools/src/pbsa/sa_driver.F90
, at least this is what is claimed here:http://archive.ambermd.org/201610/0088.html
The text was updated successfully, but these errors were encountered: