[gmx-users] %exist hydrogen bond

leila karami karami.leila1 at gmail.com
Wed Feb 23 14:43:13 CET 2011

Dear Justin

very thanks for your time and attention.

I checked my input files again. there was problem in .pdb file.

correction of .pdb file results in output file being as follows (previous
problem was solved):

#    Donor                           Acceptor                           %

      NGL1             N            SOL2225            OW         0.400
     ARG58           NH2       SOL3827            OW         43.565
     ARG58           NH2       SOL7338            OW         1.839
     ARG58           NH1       SOL2225            OW         0.080
     ARG58           NH1       SOL2253            OW          21.663
     ARG58           NH1       SOL7338            OW         0.160
     ARG58            NE       SOL3595             OW           1.359
   SOL1043            OW          GLY3              O             1.759
   SOL1043            OW          GLY4              O             0.400
   SOL1548            OW         THR47             O            61.711
   SOL1548            OW         ASN51           OD1         16.867
   SOL1548            OW         ASN51           ND2          0.320
   SOL1805            OW         GLN23           OE1         11.191
   SOL1805            OW         LEU26             O            0.160
   SOL1805            OW         SER27             N            0.160

best regards


Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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