Hi, Justin,
You are right, I should first fix the bad geometry.
I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
1 N1+ (GLY124 N) 4 H (GLY124 HT3)
181 C (PRO137 CD) 182 H (PRO137 HD1)
262 H (PHE141 HD1) 263 C (PHE141 CE2)
296 O1- (ASP144 OD2) 297 C (ASP144 C)
685 O (PRO165 O) 688 C (VAL166 CA)
for these atoms bonds that rotated more than 30 degrees
1dx0.pdb is get from NMR.
So, for the initial structure , is there anyways to solve these LINCS
WARNING ?
Thank you very much!
maggin
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