From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Aug 15 2006 - 14:21:40 CDT
Hi Dhiraj,
if you haven't also edited your topology file, then you probably don't
HAVE a PROPN patch present, which would be the problem. I'm not aware of
a deprotonated proline patch out there for the charmm forcefield; you
may be able to find one by googling a bit, or (depending on how rigorous
you want to be) create one by editing the PROP patch to have no proton
and the appropriate charges (which you can get either ideally from a QM
run, or less ideally from a similar fragment you find in a charmm or
non-charmm topology somewhere).
Peter
Dhiraj Srivastava wrote:
> hi peter
> i got this information from
> http://www.vscht.cz/fch/software/macsimus/man/pdb_2.html
> <http://www.vscht.cz/fch/software/macsimus/man/pdb_2.html>. i do not
> know much about applying patches. i have just tried it. when i was
> trying PROP then i was getting protonated form of proline.
> Dhiraj
>
>
>
> On 8/15/06, *Peter Freddolino* <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> Dear Dhiraj,
> could you let us know where you got your patch from? You have a
> "PROPN"
> patch listed in your file, but the only proline N-terminal patch
> in the
> standard charmm topology files is PROP, which is a protonated version.
> Best,
> Peter
>
> Dhiraj Srivastava wrote:
> > hi all
> > sorry for the previous incomplete mail. now i am adding my
> > psfgen script and the eroor message i got. here is the psfgen
> script.
> >
> >
> > package require psfgen
> >
> > topology top_all27_prot_lipid.inp
> >
> > topology fad_top.inp
> >
> > pdbalias residue HIS HSE
> >
> > pdbalias atom ILE CD1 CD
> >
> >
> >
> > segment A {pdb chain_A.pdb}
> >
> > coordpdb chain_A.pdb A
> >
> > segment B {pdb chain_B.pdb}
> >
> > coordpdb chain_B.pdb B
> >
> > segment P {
> >
> > patch PROPN P:2002
> >
> > pdb pro.pdb
> >
> > }
> >
> > coordpdb pro.pdb P
> >
> >
> >
> > segment F {pdb FAD.pdb}
> >
> > coordpdb FAD.pdb F
> >
> > guesscoord
> >
> > writepdb prodh1.pdb
> >
> > writepsf prodh1.psf
> >
> > exit
> >
> > and here is the error message i got.
> >
> >
> > building segment P
> >
> > applying patch PROPN to 1 residues
> >
> > ERROR: failed to apply patch
> >
> > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> >
> > ERROR: failed while building segment
> >
> > MOLECULE MISSING! Use resetpsf to start over.
> >
> > MOLECULE MISSING! Use resetpsf to start over.
> >
> > MOLECULE MISSING! Use resetpsf to start over.
> >
> > MOLECULE MISSING! Use resetpsf to start over.
> >
> > MOLECULE MISSING! Use resetpsf to start over.
> >
> > MOLECULE MISSING! Use resetpsf to start over.
> >
> >
> >
> > can you please help me out from this problem.
> >
> >
> >
> >
> > On 8/15/06, *Dhiraj Srivastava* < dhirajks_at_gmail.com
> <mailto:dhirajks_at_gmail.com>
> > <mailto:dhirajks_at_gmail.com <mailto:dhirajks_at_gmail.com>>> wrote:
> >
> > hi all
> > i am trying to apply n terminal patch on proline so that
> > the N atom is not protonated and is neutral. this proline
> is not
> > in polypeptide chain but is as a substrate of my enzyme. i have
> > tried several times but i am not able to get a proline molecule
> > with neutral amino group and a charged carboxylate group.
> how can
> > i do that. proline binds to my protein in its -vely charged
> state
> > and not in its zwiterionic form.
> >
> >
> > --
> > Dhiraj Kumar Srivastava
> > Department of Chemistry
> > University of Missouri-Columbia
> > MO, 65211
> > Ph. no. 001-573-639-0153
> >
> >
> >
> >
> > --
> > Dhiraj Kumar Srivastava
> > Department of Chemistry
> > University of Missouri-Columbia
> > MO, 65211
> > Ph. no. 001-573-639-0153
>
>
>
>
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
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