[gmx-users] CNT

[trevor brown]

Hi Justin,
I added lines to ffnonbonded.itp. It resulted in following error. It has
some warnings and an error. I am interested in error. After that I will look
at the warnings. In which file we may have an error? It is not specified.

best wishes
trevor


Generated 335790 of the 335790 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 335790 of the 335790 1-4 parameter combinations
Excluding 5 bonded neighbours molecule type 'ICE'
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 170 in topol.top and final2.gro does not match (H1 - CA)
Warning: atom name 171 in topol.top and final2.gro does not match (H2 - C)
Warning: atom name 172 in topol.top and final2.gro does not match (H3 - O)
Warning: atom name 173 in topol.top and final2.gro does not match (CA - CB)
Warning: atom name 174 in topol.top and final2.gro does not match (HA - CG)
Warning: atom name 175 in topol.top and final2.gro does not match (CB - CD1)
Warning: atom name 176 in topol.top and final2.gro does not match (HB1 -
CD2)
Warning: atom name 177 in topol.top and final2.gro does not match (HB2 - HA)
Warning: atom name 178 in topol.top and final2.gro does not match (CG - HB1)
Warning: atom name 179 in topol.top and final2.gro does not match (HG - HB2)
Warning: atom name 180 in topol.top and final2.gro does not match (CD1 - HG)
Warning: atom name 184 in topol.top and final2.gro does not match (CD2 -
HD21)
Warning: atom name 185 in topol.top and final2.gro does not match (HD21 -
HD22)
Warning: atom name 186 in topol.top and final2.gro does not match (HD22 -
HD23)
Warning: atom name 187 in topol.top and final2.gro does not match (HD23 -
H1)
Warning: atom name 188 in topol.top and final2.gro does not match (C - H2)
Warning: atom name 189 in topol.top and final2.gro does not match (O - N)
Warning: atom name 190 in topol.top and final2.gro does not match (N - CA)
Warning: atom name 191 in topol.top and final2.gro does not match (H - C)
Warning: atom name 192 in topol.top and final2.gro does not match (CA - O)
(more than 20 non-matching atom names)
WARNING 2 [file topol.top, line 39]:
  184 non-matching atom names
  atom names from topol.top will be used
  atom names from final2.gro will be ignored

There were 2 warnings
-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1356
Fatal error:
There was 1 error in input file(s)
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