Liu-group / AutoSolvate

Automated workflow for generating quantum chemistry calculation of explicitly solvated molecules

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propose a consistent naming scheme .lib files

BrandeisPatrick opened this issue · comments

commented

for generating and inputting .lib files in autosolvate
I propose

  1. use .lib instead of .off extension (these are same extensions)
  2. when creating a lib file.
    use molecule name + .lib instead of residue name + lib

unlike the following example in Setup_solvated_MD_Amber.docx
source leaprc.protein.ff14SB
source leaprc.gaff
loadamberparams solute.frcmod
LIG = loadmol2 solute.mol2
check LIG
set LIG head LIG.1.C
set LIG tail LIG.1.O1
saveoff LIG lig.lib
quit

reason:
It is easy for autosovlate Molecule class and SolventBox class to find the corresponding document.
(for detail. check update(self) class method in both of them)