From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Wed Oct 26 2005 - 11:39:44 CDT
Thanks to all who wrote with suggestions.
I finally got it to work and generated a new pdb and
psf file.
There's one last problem with this sequence, still,
though. I just realized that the first tyrosine
residue has a chlorine atom on the 3-position. So,
how do I handle that? (probably need a new topology
for tryosine-3-Cl)
Next, I want to build a peptide that has the sequence
Prop-Arg-Tyr-Tyr-Arg-Arg-Nme. In other words, Ace
becomes Prop (propyl). How does one handle that?
Thanks again,
Richard
>
> On 26 Oct 2005, at 15:26, Richard Wood wrote:
>
> > Well, if you add up the atoms of the sequence,
> using
> > NAMD/psfgen you'd get 152 atoms I believe. My pdb
> > file has 150 (including hydrogens).
> >
> > The program that I used to build the peptide
> before
> > defines NMe as NH-CH3, or six atoms, and not
> CO-NH-CH3
> > (i.e, CT3), which is 8.
> >
> > Regardless of this, the output I get tells me
> "unknown
> > residue type ACE" or "unknown residue type CT3".
> >
> > So it still doesn't work.
> >
> > here's my input:
> >
> > topology top_all22_prot.inp
> >
> > segment test { pdb VII-87-B.ent
> > first ACE
> > last CT3
> > }
> >
> > coordpdb VII-87-B.ent test
> >
> > guesscoord
> >
> > writepdb 787B.pdb
> > writepsf 787B.psf
> > exit
> >
> > And here's the output...
> >
> > Created by CHARMM version 22 1
> > building segment TEST
> > reading residues from pdb file VII-87-B.ent
> > extracted 8 residues from pdb file
> > setting patch for first residue to ACE
> > setting patch for last residue to CT3
> > Info: generating structure...
> > unknown residue type ACE
> >
> > Richard
> >
> > --- Michel Espinoza-Fonseca
> <mef_at_ddt.biochem.umn.edu>
> > wrote:
> >
> >> those are both residues and patches, and usually
> you
> >> use them the way I wrote you before... I'm not
> very
> >> clear on what you want to get (NME and CT3 are
> the
> >> same thing!). Remember that you're patching the
> >> termini, so you'll have a CO tail + the
> >> N-metylamide.
> >>
> >> If you think that this is not clear enough, take
> a
> >> look to the topology file. After the "standard"
> >> residues, you'll find the respective patches et
> al.
> >>
> >> Michel
> >>
> >> ________________________________
> >>
> >> From: owner-namd-l_at_ks.uiuc.edu on behalf of
> Richard
> >> Wood
> >> Sent: Wed 10/26/2005 7:34 AM
> >> To: namd-l_at_ks.uiuc.edu
> >> Subject: RE: namd-l: trying to generate a peptide
> >>
> >>
> >>
> >>
> >> That doesn't work either, because ACE and CT3 are
> >> PRESes and not RESIs.
> >>
> >> Besides, CT3 is CO-NH-CH3 and NOT NH-CH3. My
> >> peptide
> >> has NH-CH3 at the terminus.
> >>
> >> Richard
> >>
> >> --- Michel Espinoza-Fonseca
> >> <mef_at_ddt.biochem.umn.edu>
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> The actual patch you need to apply is ACE and
> CT3
> >>> (the first one for acetylated N-terminus, the
> last
> >>> one for N-Methylamide C terminus).
> >>> Here is an example on how to automatically patch
> >> the
> >>> termini of your peptide:
> >>>
> >>> topology toppar/top_all27_prot_na.inp
> >>> segment HPEP { pdb your_file.pdb
> >>> first ACE
> >>> last CT3
> >>> }
> >>> coordpdb your_file.pdb HPEP
> >>> guesscoord
> >>> writepdb your_output_file.pdb
> >>> writepsf your_output_file.psf
> >>>
> >>> And that's all.
> >>>
> >>> Hope it helps,
> >>>
> >>> Michel
> >>>
> >>> ________________________________
> >>>
> >>> From: owner-namd-l_at_ks.uiuc.edu on behalf of
> >> Richard
> >>> Wood
> >>> Sent: Tue 10/25/2005 8:07 PM
> >>> To: namd-l_at_ks.uiuc.edu
> >>> Subject: namd-l: trying to generate a peptide
> >>>
> >>>
> >>>
> >>> Hi all,
> >>> Now I'm trying to generate a hexapeptide using a
> >>> previoulsy created pdb file and psfgen.
> >>>
> >>> Here's the sequence of the peptide:
> >>>
> >>> Ace-Arg-Tyr-Tyr-Arg-Trp-Arg-NMe
> >>>
> >>> psfgen tells me there is no such residue as NMe
> or
> >>> Ace. I'm using top_all22_prot.inp, and there is
> an
> >> a
> >>> PRES ACE present. However, there is NO topology
> >> for
> >>> NMe, which is NH-CH3.
> >>>
> >>> The molecule should have 150 atoms. Can anybody
> >>> provide any assistance in generating the
> "correct"
> >>> residues ACE and NMe? (ACE is CH3-C=O)
> >>>
> >>> Thanks in advance,
> >>> Richard
> >>>
> >>> p.s. I've succeeded in minimizing my protein and
> >> now
> >>> I'm running 1020000 steps (1020 ps) of dynamics.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> __________________________________
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> >>>
> >>>
> >>
> >>
> >>
> >>
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>
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