protein-DNA complexes
what about enabling protein-NA complex refinement? are there any issues related to the change below I'm not aware of? it works for me.
--- a/scripts/relax_gromacs.py
+++ b/scripts/relax_gromacs.py
@@ -119,9 +119,9 @@ try:
shift = ' '.join(f'{o:.3f}' for o in (x,y,z))
else:
raise Exception("Can't determine shift")
-
+ # was <<2, 0 dumops whole system inculding eg DNA
cmds = [
- f'gmx trjconv -f {prefix}.min.temp.pdb -s em.tpr -nocenter -o {prefix}.min.temp1.pdb <<< 2',
+ f'gmx trjconv -f {prefix}.min.temp.pdb -s em.tpr -nocenter -o {prefix}.min.temp1.pdb <<< 0',
which changes the following selection:
Will write pdb: Protein data bank file
Reading file em.tpr, VERSION 2021.4 (single precision)
Reading file em.tpr, VERSION 2021.4 (single precision)
Group 0 ( System) has 5297 elements
Group 1 ( Protein) has 3929 elements
Group 2 ( Protein-H) has 1920 elements
Group 3 ( C-alpha) has 232 elements
Group 4 ( Backbone) has 696 elements
Group 5 ( MainChain) has 930 elements
Group 6 ( MainChain+Cb) has 1152 elements
Group 7 ( MainChain+H) has 1158 elements
Group 8 ( SideChain) has 2771 elements
Group 9 ( SideChain-H) has 990 elements
Group 10 ( Prot-Masses) has 3929 elements
Group 11 ( non-Protein) has 1368 elements
Group 12 ( DNA) has 1368 elements
Edited by Grzegorz Chojnowski