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

[jahanshah ashkani]

You should remove water atoms from topology file

Arneh Babakhani <ababakha at mccammon.ucsd.edu> wrote:  Hi All, thanks for the replies. I figured out the problem. I had 
fragmented water molecules in my initial structure. After deleting 
those fragments, the warning went away. Thanks!

Diana Rodriguez Ortiz wrote:
> check that the atom names match in your pdb and topology and that they match to the parameters files an atom 
> definition files (.rtp)
>
>
> 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)
>
>
> *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
> *
>
>
> -------------------------------------------------------------
> Antes ahora y siempre COLEGIO
> University of Puerto Rico at Mayaguez
> http://www.uprm.edu
> -------------------------------------------------------------
>
>
>
> 
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


		
---------------------------------
Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060611/c8cfdbb2/attachment.html>