Re: 1QSU

From: Tim Isgro (
Date: Thu Jan 15 2004 - 15:32:22 CST

Hi Uday,

You have a residues of hydroxyproline, which is not one of the 20 amino
acids, in the pdb. Thus, it is not defined in the topology file.
(It's named HYP in the pdb.) You could alter the topology file and add a
residue called HYP. Since the residue is simply a normal proline with an
'O-H' instead of an 'H' off of the gamma carbon, it might be fine to copy
the topology entry for proline and alter it accordingly. You should be
aware, however, that the partial charges may be slightly different.

Furthermore, in performing a simulation, you'd also need to add to the
parameter file accordingly. I'm not aware of any other way to solve your


On Thu, 15 Jan 2004, Uday Chippada wrote:

> Hi everybody,
> I am trying to create a psf file for the 1QSU molecule obtained from
> job=download&pdbId=1QSU&page=&pid=53931074195445
> This is the pdb file and i have used the following commands at tkcon
> in VMD to divide it into the chains A,B and C.
> set chainA [atomselect top "chain A"]
> $chainA writepdb chainA.pdb
> and similarly for chain B and C.
> The pgn file was something like this
> package require psfgen
> topology top_all27_prot_lipid.inp
> alias residue HIS HSE
> alias atom ILE CD1 CD
> segment U {pdb chainA.pdb}
> coordpdb chainA.pdb U
> guesscoord
> writepdb chainA.pdb
> writepsf chainA.psf
> I keep getting error that says couldnot write to pdb and psf files.
> Please let me know if there is a different way to create the psf file
> for molecules that exist as 3 chains.
> Am new to NAMD and have done the tutorial on Ubiquitin and have
> followed the same way for this as well.
> Any help will be appreciated
> Thanx
> Uday Chippada

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