Re: CHARMM36 and TIP3

From: Brian Radak (
Date: Tue Apr 26 2016 - 13:57:05 CDT

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.


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

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