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

[Kushal Seth]

Just in case.
The order of atoms in your gro files should match the order in the top
 files.Like if we have 1 Protein and then 1 DMPC then again 1 PROTEIN
and 1 DMPC, then top files should read as
Protein          1
 DMPC          1
Protein           1
DMPC           1
and so on...
Hope this helps.
Kushal Seth


On 6/9/06, Arneh Babakhani <ababakha at mccammon.ucsd.edu> wrote:
> No ions, it's a neutral system.
>
> The order of DMPC and Water, in what sense?
>
> In the gro file, the proteins come first, then the DMPC residues, then
> the water.
>
> The order is similar in the [system] part of my top file.
>
> Are we allowed to send attachments on this user-list? If so, I'm more
> than willing to attach my gro and top file, so you can see them in their
> entirety.
>
> thanks,
>
> Arneh
>
> David van der Spoel wrote:
> > 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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