<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<b>Hello, I'm getting the following warning when running grompp:</b><br>
<br>
<small>processing coordinates...<br>
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)<br>
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (OW - HW1)<br>
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (HW1 - HW2)<br>
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (HW2 - OW)<br>
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (OW - HW1)<br>
Warning: atom names in ../BuildInitialStructure/NoBadWater.top and
../BuildInitialStructure/NoBadWater.gro don't match (HW1 - HW2)<br>
<br>
<br>
<b>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:</b><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>
</small>. . . . . . . <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>
<b>(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? <br>
<br>
Thanks, <br>
<br>
Arneh<br>
</b>
</body>
</html>