From 6d15486e6ef9cc491fc81fe92c469d9b4e2fec76 Mon Sep 17 00:00:00 2001 From: Reecan J Juarez <43446448+so-dopamine@users.noreply.github.com> Date: Fri, 13 Oct 2023 13:34:16 -0500 Subject: [PATCH] Update Class_PDB.py fixed ASX tleap parameterization --- Class_PDB.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Class_PDB.py b/Class_PDB.py index 0a7e792..19e2ecb 100644 --- a/Class_PDB.py +++ b/Class_PDB.py @@ -833,14 +833,14 @@ def PDB2PDBwLeap(self): leap_input.write('bond a.'+ring_num+'.N a.ASX.C\n') leap_input.write('bond a.ASX.CG a.1.N\n') #isopeptide bond leap_input.write('remove a a.ASX.OD2\n') - leap_input.write('remove a a.ASX.H02\n') + leap_input.write('remove a a.ASX.HB2\n') leap_input.write('remove a a.ASX.HB3\n') - leap_input.write('remove a a.1.H1\n') - leap_input.write('remove a a.1.H2\n') - leap_input.write('remove a a.1.H3\n') - leap_input.write('remove a a.9.H1\n') - leap_input.write('remove a a.9.H2\n') - leap_input.write('remove a a.9.H3\n') + #leap_input.write('remove a a.1.H1\n') + #leap_input.write('remove a a.1.H2\n') + #leap_input.write('remove a a.1.H3\n') + #leap_input.write('remove a a.9.H1\n') + #leap_input.write('remove a a.9.H2\n') + #leap_input.write('remove a a.9.H3\n') leap_input.write('deletebond a.ASX.CG a.'+ring_num+'.N\n') leap_input.write('deletebond a.ASX.C a.2.N\n') else: @@ -874,7 +874,7 @@ def PDB2PDBwLeap(self): def partition(self): ''' - partition the lasso structure into parts -Reecan + partition the lasso structure into parts ''' a = list(self.topology_sort()) @@ -1317,7 +1317,7 @@ def _combine_parm(self, lig_parms, prm_out_path='', o_dir='', ifsavepdb=0, ifsol of.write('deletebond a.ASX.CG a.'+ring_num+'.N'+line_feed) #of.write('deletebond a.ASX.C a.2.N'+line_feed) of.write('deletebond a.ASX.O a.10.C'+line_feed) - of.write('remove a a.ASX.OXT'+line_feed) + #of.write('remove a a.ASX.OXT'+line_feed) of.write('remove a a.ASX.OD2'+line_feed) of.write('remove a a.ASX.H01'+line_feed) of.write('deletebond a.ASX.OD1 a.10.N'+line_feed)