[AMBER] ParmEd: tiMerge error with ff19SB CMAP term

From: Ali Morshedi <morshedi1370.gmail.com>
Date: Thu, 18 Nov 2021 01:06:54 -0800

Hi all,

tiMerge gives an error when used with ff19SB as documented here:

I think the issue comes from the fact that in "actions.py" line 2437, if
atm1 belongs to a cmap involving atm2, it should be kept as well (similar
to what is done for bonds, angles and dihedrals). I made the following

if (atm1 in atm2.bond_partners or atm1 in atm2.angle_partners or
       atm1 in atm2.dihedral_partners):
    keep_mask[i] = 1
for x in atm2.cmaps:
    if atm1 in [x.atom1, x.atom2, x.atom3, x.atom4, x.atom5]:
        keep_mask[i] = 1

It may not be the most efficient, but things seem to be running ok. I was
wondering if you could let me know if you see any problems with this fix.


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Received on Thu Nov 18 2021 - 01:30:02 PST
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