Dear Amber developers,
The tiMerge works well with the ff14SB force fields. However when I use the
tiMerge with the ff19SB force field, I come across a severe problem as the
following.
*Traceback (most recent call last):*
* File "/share/apps/amber20_src/bin/parmed", line 33, in <module>*
* sys.exit(load_entry_point('ParmEd==3.4.1', 'console_scripts',
'parmed')())*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/scripts.py",
line 200, in clapp*
* parmed_commands.cmdloop()*
* File "/share/apps/amber20_src/miniconda/lib/python3.8/cmd.py", line 138,
in cmdloop*
* stop = self.onecmd(line)*
* File "/share/apps/amber20_src/miniconda/lib/python3.8/cmd.py", line 217,
in onecmd*
* return func(arg)*
* File "<string>", line 1, in <lambda>*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/tools/parmed_cmd.py",
line 161, in _normaldo*
* action.execute()*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/tools/actions.py",
line 2610, in execute*
* self.parm.strip(remove_str)*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/amber/_amberparm.py",
line 713, in strip*
* super(AmberParm, self).strip(selection)*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/structure.py",
line 823, in strip*
* self.prune_empty_terms()*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/structure.py",
line 734, in prune_empty_terms*
* self._prune_empty_cmaps()*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/structure.py",
line 3169, in _prune_empty_cmaps*
* cmap.delete()*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/topologyobjects.py",
line 3181, in delete*
* _delete_from_list(self.atom2.cmaps, self)*
* File
"/share/apps/amber20_src/lib/python3.8/site-packages/ParmEd-3.4.1-py3.8-linux-x86_64.egg/parmed/topologyobjects.py",
line 225, in _delete_from_list*
* list.pop(list.index(item))*
*ValueError: <Cmap; <Atom C [3013]; In LYS 345>--<Atom N [2356]; In GLY
152>--<Atom CA [2358]; In GLY 152>--<Atom C [2361]; In GLY 152>--<Atom N
[-1]>; type=<CmapType; resolution=24>> is not in list*
My input script is like
*#!/bin/sh*
*#*
*#*
*parmed protein_solv.prmtop <<_EOF*
*loadRestrt protein_solv.inpcrd*
*setOverwrite True*
*tiMerge :1-194 :195-388 :152 :346*
*outparm merged_protein_solv.prmtop merged_protein_solv.inpcrd*
*quit*
*_EOF*
*parmed complex_solv.prmtop <<_EOF*
*loadRestrt complex_solv.inpcrd*
*setOverwrite True*
*tiMerge :1-791 :792-1582 :749 :1540*
*outparm merged_complex_solv.prmtop merged_complex_solv.inpcrd*
*quit*
*_EOF*
Is there anything else to do when using ff19SB ? Thanks for your help !
Best,
Jinfeng
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Received on Sat Oct 22 2022 - 01:00:03 PDT
