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 <[EMAIL PROTECTED]> 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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>
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