Constraint warning with AMBER PDB file

yimanu duu... at gmail.com
Thu Feb 11 22:38:44 CET 2010


Thanks!

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  
> way:
>
> MOLECULE 1..15
>
> I have no clue if you really have 15 molecules in your input or just 2.
> This should fix your problem.
> Teo
>
> 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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