Constraint warning with AMBER PDB file

Lekpa Duukori duu... at
Thu Feb 11 19:46:40 UTC 2010

Hi all,

I have been getting this warning  when I try to run a calculation using PDB
and topology files generated by AMBER.
The idea was to apply a constraint to the HBONDS

 *** 12:36:25 WARNING in topology_constraint_util:print_warning_molname
 *** err=-300   MOLNAME (MOL) was defined for constraints, but this
 *** molecule name is not defined. Please check carefully your PDB, PSF
 *** (has priority over PDB) or input driven CP2K coordinates. In case you
 *** may not find the reason for this warning it may be a good idea to
 *** print all molecule information (including kind name) activating the
 *** print_key MOLECULES specific of the SUBSYS%PRINT section.
 *** /opt/cp2k/makefiles/../src/topology_constraint_util.F line   1374

Using the print key it talks about prints gives molecule names like MOL0
etc, all other parameters appear to be read correctly though.

The cp2k executable I am using is about a day old.

Inputs has been uploaded to the site

Any ideas is appreciated, thanks.


PS: this is s test that reproduces an error I am getting with different
input files
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