[CP2K:480] Re: Reading topology file

Teodoro Laino teodor... at gmail.com
Thu Dec 13 00:51:08 CET 2007


Hi Chris,

a simple and additional comment to the one of Axel:
I'm sorry to say that just reporting an error without providing ALL  
the files in order to reproduce the error is most of the times useless.
There are several reasons why you may have hit into this problem,  
even a possible bug in the code.
Unfortunately if we don't work on the same files and cannot reproduce  
the same error we can't say too much. I highly suggest to all the  
people asking for help to provide ALL input files (i.e. input  + all  
the additional files necessary to run it).

cheers,
teo

On 12 Dec 2007, at 20:15, Axel wrote:

>
> On Dec 12, 1:34 pm, Chris <christopher... at chem.ox.ac.uk>
> wrote:
>> Hi,
>
> hi chris,
>
>>
>> I am trying to read into CP2K .pdb and .psf files for a system, but I
>> get the message:
>>
>>  *****************************************
>>  *** ERROR in topology_molecules_check ***
>>  *****************************************
>>
>>  *** different atom name for same molecule kind molecule type  =
>> 5 ***
>>  *** molecule number=      2 expected atom name=OCL
>> found=CTL2          ***
>
>
>> I have checked my input .psf file, and I only have one type of
>
> how did you generate your pdb/psf file. please keep in mind,
> that you cannot expect that if your input works with one package
> that it'll work with a different one just as well. many are
> "broken" in very unique ways. it also matters as what you read
> in files (there is UPSF and PSF for example).
>
> however, it is also possible, that your compiler miscompiled the
> code. i remember seeing similar error messages when i was on a
> machine that had PGI 6.2.x compilers and those went away when they
> were upgraded to 7.0.2. i'm now always compiling a g95 based
> version on top of the system default compilers, so that if there
> are input errors, i can do a cross check with an unrelated compiler.
>
>> molecule containing atoms of type OCL.  In the .psf file, all of the
>> occurrences of atoms with the name OCL occur in the same place
>> relative to the other atoms in the molecule they are in, and the  
>> atoms
>> in the .psf file are (so far as I can tell) in exactly the same order
>> as they are in the .pdb file.
>
> you may want to override the atom "name" in the pdb file with
> the atom "type" from the .psf file. to do this with VMD:
>
> set mol [mol new "input.psf"]
> mol addfile $mol "input.pdb"
> set sel [atomselect $mol all]
> $sel set name [$sel get type]
> $sel writepdb "input-new.pdb"
>
> hope that helps,
>     axel.
>>
>> Please could someone explain this error message?
>>
>> Thanks,
>>
>> Chris
> >




More information about the CP2K-user mailing list