Constraint warning with AMBER PDB file
duu... at gmail.com
Thu Feb 11 22:38:44 CET 2010
On Feb 11, 1:41 pm, Laino Teodoro <teodor... at gmail.com> wrote:
> Dear Lepka,
> unfortunately AMBER topology files do not have any information about
> molecule names. What is stored there is the residue name, which we
> don't really use within CP2K.
> As you realized CP2K is assigning new molname: MOL01..
> You can either specify the whole list within the appropriate molname
> keyword or alternatively just use the other keyword MOLECULE in this
> MOLECULE 1..15
> I have no clue if you really have 15 molecules in your input or just 2.
> This should fix your problem.
> p.s.: just a comment: please upload 1 unique tar (gzipped) file: this
> makes life easier.
> On 11 Feb 2010, at 20:46, Lekpa Duukori wrote:
> > 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.
> > Lekpa
> > PS: this is s test that reproduces an error I am getting with
> > different input files
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