From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 26 2016 - 19:49:04 CDT
Hi Dhiraj,
You are right. Stream files need to be pruned before using them with
psfgen, since it doesn't know how to ignore parameter lines and throws
the error you are seeing. For toppar_water_ions.str, I actually split it
into two files, the topology part, and the parameter part, taking care
to remove lines that are CHARMM specific (like setting bomlevs or if
statements)
-Josh Vermaas
On 04/26/2016 05:01 PM, Dhiraj Srivastava wrote:
> Thanks Brian
> the errors that I am getting are
> psfgen) ERROR! Failed to parse autogenerate statement.
>
> and
>
> psfgen) ERROR! FAILED TO RECOGNIZE NONBONDED
> psfgen) ERROR! FAILED TO RECOGNIZE cutnb
> psfgen) ERROR! FAILED TO RECOGNIZE HT
> psfgen) ERROR! FAILED TO RECOGNIZE OT
> psfgen) ERROR! FAILED TO RECOGNIZE OX
> psfgen) ERROR! FAILED TO RECOGNIZE HX
> psfgen) ERROR! FAILED TO RECOGNIZE LIT
> psfgen) ERROR! FAILED TO RECOGNIZE SOD
> psfgen) ERROR! FAILED TO RECOGNIZE MG
> psfgen) ERROR! FAILED TO RECOGNIZE POT
>
> and so on.
>
> I think its something related to formatting of topology file,
> specially stream file.
>
> Dhiraj
>
>
> On Tue, Apr 26, 2016 at 1:57 PM, Brian Radak <bradak_at_anl.gov
> <mailto:bradak_at_anl.gov>> wrote:
>
> Is it actually an error or just a warning. If you have multiple
> RESI or PRES definitions with the same name (as is common in the
> way the CHARMM community has organized the force field) then this
> makes sense. I believe psfgen will always use the first definition
> so that the order in which you call "topology" will matter. The
> only other question then is whether or not the atom type has been
> declared before it is used in a RESI definition.
>
> HTH,
> Brian
>
>
> On 04/26/2016 01:37 PM, Dhiraj Srivastava wrote:
>> Hi All
>> I am trying to generate psf file using psfgen in vmd. its
>> working fine with protein only ( when using top_all36_prot.rtf
>> only) but when I am trying it with water, I have to provide
>> toppar_water_ions.str (stream) file and I start seeing error like
>> "duplicate type key" and "duplicate residue key". this problem
>> does not happen with charmm22 and 27. unfortunately I have to use
>> CHARMM36 because one of my ligand is carbohydrate. How can solve
>> this problem?
>>
>> Thanks
>> Dhiraj
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643 <tel:%28630%29%20252-8643>
> brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
>
>
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