[AMBER] tiMerge error with ff19SB

From: HOCHEOL LIM <ihcdatabank.gmail.com>
Date: Wed, 10 Jun 2020 17:30:47 +0900

Dear All,

There are errors in tiMerge with ff19SB.
When I changed ff19SB to ff14SB, it worked.

I copied the error message.

In pdb file, there is no ASP137 and LEU30, but GLN137 and ALA30 (LEU31).
I tried to make a mask between ALA30 and ASP138.

Thank you.

  Traceback (most recent call last):
  File "/opt/amber20/bin/parmed", line 6, in <module>
  File "/opt/amber20/lib/python3.7/site-packages/parmed/scripts.py", line
200, in clapp
  File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
    stop = self.onecmd(line)
  File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
    return func(arg)
  File "<string>", line 1, in <lambda>
"/opt/amber20/lib/python3.7/site-packages/parmed/tools/parmed_cmd.py", line
161, in _normaldo
  File "/opt/amber20/lib/python3.7/site-packages/parmed/tools/actions.py",
line 2610, in execute
"/opt/amber20/lib/python3.7/site-packages/parmed/amber/_amberparm.py", line
714, in strip
    super(AmberParm, self).strip(selection)
  File "/opt/amber20/lib/python3.7/site-packages/parmed/structure.py", line
824, in strip
  File "/opt/amber20/lib/python3.7/site-packages/parmed/structure.py", line
735, in prune_empty_terms
  File "/opt/amber20/lib/python3.7/site-packages/parmed/structure.py", line
3170, in _prune_empty_cmaps
"/opt/amber20/lib/python3.7/site-packages/parmed/topologyobjects.py", line
3181, in delete
    _delete_from_list(self.atom2.cmaps, self)
"/opt/amber20/lib/python3.7/site-packages/parmed/topologyobjects.py", line
225, in _delete_from_list
ValueError: <Cmap; <Atom C [1710]; In ASP 137>--<Atom N [471]; In LEU
30>--<Atom CA [473]; In LEU 30>--<Atom C [488]; In LEU 30>--<Atom N [-1]>;
type=<CmapType; resolution=24>> is not in list
AMBER mailing list
Received on Wed Jun 10 2020 - 02:00:03 PDT
Custom Search