[gmx-users] CNT

[Mark Abraham]

On 20/01/2011 10:51 AM, trevor brown wrote:
> 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)

Atom orders must match. The existence of any warning causes an error.

Mark