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

[Arneh Babakhani]

*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
*
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