Re: CHARMM36 and TIP3

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Apr 26 2016 - 17:01:10 CDT

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> 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
> brian.radak_at_anl.gov
>

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