From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Oct 06 2005 - 15:22:01 CDT
You can also find an example of applying patches to a protein in the
BPTI example from the NAMD manual, under the "Creating PSF Structure
Files" section.
Peter
Anna Modzelewska wrote:
> 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 <mailto:rwoodphd_at_yahoo.com>
> *To:* Anna Modzelewska <mailto:amodzelewska_at_iimcb.gov.pl>
> *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
> <mailto: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
> <mailto: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 <mailto: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 <mailto: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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> === message truncated ===
>
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