[CP2K:2545] Constraint warning with AMBER PDB file

Laino Teodoro teodor... at gmail.com
Thu Feb 11 21:41:57 CET 2010


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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