[gmx-users] grompp warnings...

[Dallas Warren]

Eva,

>WARNING 1 [file "C:/gromacs/share/top/ffgmx.itp", line 6]:
>   Found another defaults entry, will use the last one

This means that it found more than one entry in the force field files for 
the same thing.  When it encounters two lines defining the same thing, 
whether it is atom types, bonds, dihedrals etc, then the program uses the 
last one defined.

>Warning: atom names in pro_lip.top and pro_lip.gro don't match (CN1 - CA)
>Warning: atom names in pro_lip.top and pro_lip.gro don't match (CN2 - CB)

This error came up a week or two ago on the list, I think.  May be check 
the archive.  I think it has to do with the order in which the included 
topologies are in the topology file.  I encountered something very similar 
to this (can't recall the error exactly), but simply changing the order of 
the molecules in the list at the end of the topology file fixed it.

Hope that is of some assistance.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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