From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Oct 07 2005 - 10:18:02 CDT
Richard,
could you post the complete psfgen output that you get? Things should be
working ok now that you have gotten rid of the outdated terminus (I
believe that the alanin.pdb was originally generated in 1989).
Peter
Anna Modzelewska wrote:
> 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 <mailto:rwoodphd_at_yahoo.com>
> *To:* Anna Modzelewska <mailto:amodzelewska_at_iimcb.gov.pl>
> *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
> <mailto: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
> <mailto: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 <mailto: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 <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
> >
> === message truncated ===
>
>
>
>
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