Hi,
I keep wondering why in the attached code the setbond class creates a new bond type (with proper linkage) as expected but the same doesn't seem to work for setangle. The output parm mod.parm7 appears to have effectively the same angle entries.
Many thanks,
Hannes.
from chemistry.amber.readparm import AmberParm
import ParmedTools.ParmedActions as pact
parm = AmberParm('test.parm7')
atom_name = parm.parm_data['ATOM_NAME']
for atom in parm.atom_list:
idx = atom.starting_index
if atom_name[idx].startswith('DU'):
for bond in atom.bonds:
idx1 = bond.atom1.starting_index + 1
idx2 = bond.atom2.starting_index + 1
act = pact.setbond(parm, '.%i .%i %f %f' % (idx1, idx2, 99.9, 0.999) )
act.execute()
if atom_name[idx].startswith('DU'):
for ang in atom.angles:
idx1 = ang.atom1.starting_index + 1
idx2 = ang.atom2.starting_index + 1
idx3 = ang.atom3.starting_index + 1
act = pact.setangle(parm, '.%i .%i .%i %f %f' % (idx1, idx2, idx3,
99.9, 99.9) )
act.execute()
parm.overwrite = True
parm.writeParm('mod.parm7')
--
Scanned by iCritical.
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- application/octet-stream attachment: mod.parm7
Received on Wed Mar 26 2014 - 08:30:03 PDT
