You should remove water atoms from topology file<BR><BR><B><I>Arneh Babakhani <ababakha@mccammon.ucsd.edu></I></B> wrote: <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi All, thanks for the replies. I figured out the problem. I had <BR>fragmented water molecules in my initial structure. After deleting <BR>those fragments, the warning went away. Thanks!<BR><BR>Diana Rodriguez Ortiz wrote:<BR>> check that the atom names match in your pdb and topology and that they match to the parameters files an atom <BR>> definition files (.rtp)<BR>><BR>><BR>> Arneh Babakhani <ABABAKHA@MCCAMMON.UCSD.EDU>wrote: <BR>> *Hello, I'm getting the following warning when running grompp:*<BR>><BR>> processing coordinates...<BR>> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and <BR>> ../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)<BR>> Warning: atom names in
../BuildInitialStructure/NoBadWater.top and <BR>> ../BuildInitialStructure/NoBadWater.gro don't match (OW - HW1)<BR>> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and <BR>> ../BuildInitialStructure/NoBadWater.gro don't match (HW1 - HW2)<BR>> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and <BR>> ../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)<BR>> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and <BR>> ../BuildInitialStructure/NoBadWater.gro don't match (OW - HW1)<BR>> Warning: atom names in ../BuildInitialStructure/NoBadWater.top and <BR>> ../BuildInitialStructure/NoBadWater.gro don't match (HW1 - HW2)<BR>><BR>><BR>> *I can't seem to find where the discrepancy is between by top file and <BR>> structure file. Here's an excerpt from my top file:*<BR>><BR>> ; Include forcefield parameters<BR>> #include "ffgmx.itp"<BR>> #include "lipid.itp"<BR>> ; Include
topologies<BR>> #include "dmpc.itp"<BR>> #ifdef FLEX_SPC<BR>> #include "flexspc.itp"<BR>> #else<BR>> #include "spc.itp"<BR>> #endif<BR>> [ moleculetype ]<BR>> ; Name nrexcl<BR>> Protein 3<BR>> . . . . . . .<BR>> [ system ]<BR>> ; Name<BR>> My membrane with peptides in water<BR>> [ molecules ]<BR>> ; Compound #mols<BR>> Protein 2<BR>> DMPC 128<BR>> SOL 6636<BR>><BR>> *(I purposely cut out the atoms and such of "Protein", b/c it's not <BR>> relevant here). This worked previously, so I'm not sure what's going on <BR>> here, any suggestions?<BR>><BR>> Thanks,<BR>><BR>> Arneh<BR>> *<BR>><BR>><BR>> -------------------------------------------------------------<BR>> Antes ahora y siempre COLEGIO<BR>> University of Puerto Rico at Mayaguez<BR>> http://www.uprm.edu<BR>> -------------------------------------------------------------<BR>><BR>><BR>><BR>>
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