Inconsistency between SOMD input files produced by BSS and by FESetup

[jmichel80]

In this example the molecule 17 is mapped to molecule 8. In line with expected behaviour for SOMD hydrogen atom H21 in 17to8 perturbation should have an atomic mass of 12 g/mol in the parm file since it is perturbed to a carbon atom.

This is indeed the case in the FEP input produced by FESetup, whereas the one produced by BSS (via https://github.com/michellab/BioSimSpace/tree/devel/nodes/playground/prepareFEP.ipynb) has not updated the atomic masses (I thought we had fixed this previously?).

The atomic mass is element number 21 in the arrays below (first number on the fifth line)

Excerpt from fesetup/tyk_lig17~tyk_lig8/solvated/solvated.parm7
%FLAG MASS
%FORMAT(5E16.8)
  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01
  1.20100000E+01  3.54500000E+01  1.20100000E+01  1.60000000E+01  1.40100000E+01
  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.40100000E+01  1.20100000E+01
  1.20100000E+01  1.40100000E+01  1.20100000E+01  1.60000000E+01  3.54500000E+01
  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00

Excerpt from bss/tyk_lig17~tyk_lig8/solvated/tyk_lig17~tyk_lig8_free.prm7
%FLAG MASS
%FORMAT(5E16.8)
   1.20100000E+1   1.20100000E+1   1.20100000E+1   1.20100000E+1   1.20100000E+1
   1.20100000E+1   3.54500000E+1   1.20100000E+1   1.60000000E+1   1.40100000E+1
   1.20100000E+1   1.20100000E+1   1.20100000E+1   1.40100000E+1   1.20100000E+1
   1.20100000E+1   1.40100000E+1   1.20100000E+1   1.60000000E+1   3.54500000E+1
   1.00800000E+0   1.00800000E+0   1.00800000E+0   1.00800000E+0   1.00800000E+0

I have attached a zip file with the FESEtup and BSS topologies, and a folder that contains the topologies of the two ligands before perturbation.

17-8.zip

[lohedges]

Sure thing, I'll add that in. I'll also attempt to add a "debug" mode that prints out exactly what is done when writing the pert file.

[lohedges]

Closing as this has been fixed.