[gmx-users] LINCS problem

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 25 00:58:42 CET 2008

s lal badshah wrote:
> Dear Experts,
> I checked the error lincs page and from that what I ignored in my work 
> are the two errors these are:
> Warning: there  are 0 atoms with zero occupancy and 1 atom with 
> occupancy unequal  to one (out of 1480 atoms).Check your pdb file
> Warning: masses will be determined based on residue and atom names,this 
> can deviate from the real mass of the atom type.In case you use free 
> energy of solvation predictions.
> Can I correct these errors?

Yes, you can. Nobody else can, because they don't know anything about 
your system. You should look on the RCSB page for a description of the 
PDB file format to see where occupancy is described so that you can 
determine what the non-one occupancy is all about.


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