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

[Arneh Babakhani]

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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