[gmx-users] Re: distance_restraints

maggin maggin.chen at gmail.com
Wed Jun 12 06:10:04 CEST 2013

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

Thank you very much!


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