[gmx-users] grompp warning: atom names don't match - with respect to solvent

[Arneh Babakhani]

Hi All, thanks for the replies. I figured out the problem. I had 
fragmented water molecules in my initial structure.  After deleting 
those fragments, the warning went away. Thanks!

Diana Rodriguez Ortiz wrote:
> check that the atom names match in your pdb and topology and that they match to the parameters files an atom 
> definition files  (.rtp)
>
>
> Arneh Babakhani <ababakha at mccammon.ucsd.edu> wrote: 
> *Hello, I'm getting the following warning when running grompp:*
>
> processing coordinates...
> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and 
> ../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)
> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and 
> ../BuildInitialStructure/NoBadWater.gro don't match (OW - HW1)
> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and 
> ../BuildInitialStructure/NoBadWater.gro don't match (HW1 - HW2)
> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and 
> ../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)
> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and 
> ../BuildInitialStructure/NoBadWater.gro don't match (OW - HW1)
> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and 
> ../BuildInitialStructure/NoBadWater.gro don't match (HW1 - HW2)
>
>
> *I can't seem to find where the discrepancy is between by top file and 
> structure file.  Here's an excerpt from my top file:*
>
> ; Include forcefield parameters
> #include "ffgmx.itp"
> #include "lipid.itp"
> ; Include topologies
> #include "dmpc.itp"
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> [ moleculetype ]
> ; Name            nrexcl
> Protein           3
> . . . . . . .
> [ system ]
> ; Name
> My membrane with peptides in water
> [ molecules ]
> ; Compound        #mols
> Protein          2
> DMPC             128
> SOL              6636
>
> *(I purposely cut out the atoms and such of "Protein", b/c it's not 
> relevant here).  This worked previously, so I'm not sure what's going on 
> here, any suggestions?
>
> Thanks,
>
> Arneh
> *
>
>
> -------------------------------------------------------------
> 	Antes ahora y siempre COLEGIO
> 	University of Puerto Rico at Mayaguez
> 	http://www.uprm.edu
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>
>
>
>