[CP2K:1025] Re: input coordinates & charges

Teodoro Laino teodor... at gmail.com
Mon May 12 10:43:20 UTC 2008

Dear Csilla,

First of all let's say that there's no difference if you use cp2k  
standalone of you invoke it from another program.
Our convention is quite clear about it: a kind has a well defined  
charge. I.e. you can't provide an array of different charges
associated to the same kind.

The problem is in the definition of your problem.

So if you want some help, we need more details.
How did you generated the CHARMM parameter file? is it one of the  
standard publicly distributed?
or you generated it with external tools starting maybe from other  
brand topology files?
are you also providing a PSF or you rely on the internal topology  

I rarely used PSFGEN, so I cannot comment how helpful it would be in  
solving this problem.. But essentially,
with some lines of scripting, you can do the type conversion without  
getting mad (both for PDB, parameter file and so).

let us know withe above informations if you need further help!


On 12 May 2008, at 12:19, Csilla Varnai wrote:

> I must confess I have not tried the VMD psfgen, since I would like  
> to invoke CP2K from another program, and that is the reason why I  
> would like to avoid the use of other programs like the VMD psfgen.  
> If I used the cp2k f77_interface, would it make any difference  
> concerning to this problem? Should I also have a potential file  
> containing atomic types with unambiguously defined charges? If that  
> is the case then I run into the same memory problem. Does the  
> psfgen seem to be the only solution?

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