Re: help generating psf files

From: Anna Modzelewska (amodzelewska_at_iimcb.gov.pl)
Date: Thu Oct 06 2005 - 08:55:18 CDT

Indeed, ACE means that the N-term is acetylated. CBX is also a modification of the protein. They are not classic residues that's why psfgen can not find them in the residues section of the topology file. If you remove these two residues from your pdb and you try to create the psf in the same the way as usually you should success in.
You can find ACE at the end of the topology file in the section with "patches".
I recommend you to read the C Appendix of Namd Tutorial, the construction of topology file is well explained there.
If you still have problems with psfgen let me know.

Anna

----- Original Message -----
  From: Richard Wood
  To: Anna Modzelewska
  Sent: Thursday, October 06, 2005 3:30 PM
  Subject: Re: namd-l: help generating psf files

  Well, the residue ACE is incorrect in the file.
  It consists of three atoms: CA, C and O.
  I assume that residue CBX (N, H, CA) is incorrect
  also.

  Richard

  --- Anna Modzelewska <amodzelewska_at_iimcb.gov.pl>
  wrote:

> Now, I'm sure that your pdb file is problematic,
> could you send it to me? Do you have some
> non-standard residues that you want to keep (as ACE
> for example or some phosphorylated residues) in the
> structure?
>
> Anna
> ----- Original Message -----
> From: Richard Wood
> To: Anna Modzelewska
> Sent: Thursday, October 06, 2005 3:12 PM
> Subject: Re: namd-l: help generating psf files
>
>
> hi Anna,
>
> It looks like it might be something to do with the
> residue names, as when I type in segment ala { pdb
> alanin.pdb }, it gives messages "unknown residue
> type
> CBX" and "unknown residue type ACE". Please note
> that
> this pdb file is one generated by the people that
> develop NAMD. If I use their alanine parameters
> and
> this pdb file to run dynamics, it works fine. I
> tried
> to generaste a psf of this file because I had
> tried
> others (my own pdb files) and I got similar errors
> when running psfgen.
>
> Richard
>
> --- Anna Modzelewska <amodzelewska_at_iimcb.gov.pl>
> wrote:
>
> > Hi Richard,
> > I'm not an expert, but that's what I would try
> to
> > type:
> >
> > topology top_all22_prot.inp
> > segment ala { pdb alanin.pdb }
> > coordpdb alanin.pdb ala
> > guesscoord
> > writepdb alanin1.pdb
> > writepsf alanin.psf
> >
> > Remeber that you should precise the paths for
> files
> > that you use (pdb and topology file).
> > The comment "Created by CHARMM version 22 1" is
> > normal so I think that something else is wrong.
> > Probably there is a problem with your pdb file.
> > Please try to generate a psf for alanin with the
> > commands above and let me know if it works. What
> > version of VMD or NAMD do you use?
> >
> > Anna
> > ----- Original Message -----
> > From: Richard Wood
> > To: Anna Modzelewska
> > Sent: Thursday, October 06, 2005 2:47 PM
> > Subject: Re: namd-l: help generating psf files
> >
> >
> > Hi Anna,
> >
> > Well, all I did was run psfgen interactively.
> I
> > didn't use a script.
> >
> > First, I typed in topology top_all22_prot.inp
> >
> > (Note: when I do this, the output on the
> screen
> > ends
> > with "Created by CHARMM version 22 1", and if
> I
> > type
> > toplogy top_all22_prot.inp again, the text on
> the
> > screen goes as far as the line "duplicate
> residue
> > key
> > LIG3 will be ignored")
> >
> > Then, coordpdb alanin.pdb
> >
> > When I do this, it gives me the following for
> each
> > atom : "Warning: failed to set coordinate for
> atom
> > CA
> > CBX12 MAIN" (this is the last line for the
> last
> > atom)
> >
> > Finally, I type in writepsf test.psf, which
> gives
> > the
> > following output:
> > "total of 0 atoms
> > total of 0 bonds
> > total of 0 angles
> > total of 0 dihedrals
> > total of 0 impropers
> > Info: psf file comple."
> > (which it's not)
> >
> > This is so simple it should work, but it
> doesn't.
> >
> > Richard
> >
> >
> > --- Anna Modzelewska
> <amodzelewska_at_iimcb.gov.pl>
> > wrote:
> >
> > > Richard,
> > > I've just tried and didn't have any problems
> > with
> > > creation of psf using the top_all22_prot.inp
> > file.
> > >
> > > Could you send the script that you use as
> the
> > input
> > > for psfgen and the output with error?
> > >
> > > Anna
> > > ----- Original Message -----
> > > From: Richard Wood
> > > To: namd-l_at_ks.uiuc.edu
> > > Sent: Tuesday, October 04, 2005 6:37 PM
> > > Subject: namd-l: help generating psf files
> > >
> > >
> > > I've just started using NAMD and VMD.
> I've
> > run
> > > the
> > > alanine example and it runs fine.
> However,
> > when I
> > > try
> > > to run something new, I can't create a psf
> > using
> > > psfgen. I've discovered that the problem
> is
> > in
> > > the
> > > reading of the file top_all22_prot.inp,
> which
> > I
> > > obtained from Alex Mackerrel's web site.
> > >
> > > Is there a trick to getting psfgen to read
> > this
> > > file?
> > > I have even tried to read this file in and
> > > generate a
> > > psf for alanine from alanin.pdb, but it
> can't
> > find
> > > the
> > > coordinates.
> > >
> > > What am I doing incorrectly?
> > >
> > > Richard
> > >
> > >
> > >
> > >
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> >
> >
> >
> >
>
>
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