Re: help generating psf files

From: Anna Modzelewska (amodzelewska_at_iimcb.gov.pl)
Date: Fri Oct 07 2005 - 09:16:57 CDT

I tried it with namd 2.5b1 and namd 2.5
Both scripts work with both versions of namd.

I really don't know what's wrong.
Anna
  ----- Original Message -----
  From: Richard Wood
  To: Anna Modzelewska
  Sent: Friday, October 07, 2005 4:05 PM
  Subject: Re: namd-l: help generating psf files

  That's weird because I do this with both psfgen for
  NAMD 2.5 and NAMD 2.6 and I get pdb files having
  zeroes for all the coordinates.

  Richard

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

> I took the pdb file that you sent me, I removed ace
> and cbx entries and I typed:
>
> topology ../../pola_sil/toppar/top_all22_prot.inp
> segment ala { pdb ../../alanina/alanin.pdb
> first ace
> last ct3 }
> coordpdb ../../alanina/alanin.pdb ala
> guesscoord
> writepdb ../../alanina/alanin1.pdb
> writepsf ../../alanina/alanin1.psf
>
> The alanin1.pdb and alanin1.psf files are absolutely
> correct and complete.
> ----- Original Message -----
> From: Richard Wood
> To: Anna Modzelewska
> Sent: Friday, October 07, 2005 3:36 PM
> Subject: Re: namd-l: help generating psf files
>
>
> These "scripts" writes a file but all the
> coordinates
> are zeroes, whether you do 1) or 2).
>
> Richard
>
> --- Anna Modzelewska <amodzelewska_at_iimcb.gov.pl>
> wrote:
>
> > Richard,
> > as far as I know this pdb is a result of the
> > structure generation with an older topology file
> (it
> > could be toph19.inp). The ace and cbx in that
> > topology file were residues, now they are
> patches.
> > In addition that top file used only the polar
> > hydrogens.
> > If you want to create your pdb and psf for
> > deca-alanin with acetylated and N-methylamidated
> > terminus using the topology of charm22, I know
> two
> > ways to do it:
> >
> > 1) You can remove ace and cbx entries from this
> pdb
> > and you have to modify one command:
> > segment hin { pdb alanin.pdb
> > first ace
> > last ct3 }
> > In this way psfgen will add missing atoms and
> will
> > correctly transform the terminus of the peptide.
> > That's what I would do.
> >
> > 2) If you absolutely want to keep terminus
> > coordinates from this pdb, you can modify its 6
> > entries:
> > ATOM 1 CAY ACE 2 -2.184 0.591
> > 0.910 1.00 7.00 MAIN
> > ATOM 2 CY ACE 2 -0.665 0.627
> > 0.966 1.00 0.00 MAIN
> > ATOM 3 OY ACE 2 -0.069 1.213
> > 1.868 1.00 0.00 MAIN
> > ATOM 64 NT CBX 11 8.610 8.962
> > 9.714 1.00 0.00 MAIN
> > ATOM 65 H CBX 11 8.050 8.324
> > 9.225 1.00 0.00 MAIN
> > ATOM 66 CAT CBX 11 9.223 8.571
> > 11.014 1.00 0.00 MAIN
> > Then use the same modification for segment line
> as
> > above and in the lines before type:
> > alias residue ace ala
> > alias residue cbx ala
> >
> > I hope I answered your question.
> > Anna
> >
> > ----- Original Message -----
> > From: Richard Wood
> > To: Anna Modzelewska
> > Sent: Thursday, October 06, 2005 4:48 PM
> > Subject: Re: namd-l: help generating psf files
> >
> >
> > I guess the question I now have is since the
> NAMD
> > people used this pdb file to generate a psf
> file,
> > how
> > did they do it?
> >
> > Also, ACE should be COCH3, not COC.
> >
> > I'm very familiar with topology files, as I
> used
> > CHARMm for two years, and will most likely be
> > using it
> > again soon.
> >
> > Richard
> >
> > --- Anna Modzelewska
> <amodzelewska_at_iimcb.gov.pl>
> > 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
> > > 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
>
  === message truncated ===

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