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

[David van der Spoel]

Arneh Babakhani 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)

check order of DMPC and water. Don't you have ions?

> 
> 
> *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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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