RE: trying to generate a peptide

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Wed Oct 26 2005 - 09:26:48 CDT

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.
> >
> >
> >
> >
> >
> > __________________________________
> > Yahoo! FareChase: Search multiple travel sites in
> > one click.
> > http://farechase.yahoo.com
> >
> >
> >
>
>
>
>
> __________________________________
> Yahoo! FareChase: Search multiple travel sites in
> one click.
> http://farechase.yahoo.com
>
>
>

        
                
__________________________________
Yahoo! Mail - PC Magazine Editors' Choice 2005
http://mail.yahoo.com

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:17 CST