[gmx-users] naive question about the c-terminus
Justin A. Lemkul
jalemkul at vt.edu
Mon May 10 18:08:26 CEST 2010
abdullah ahmed wrote:
> The gromacs version is 3.3.1, which I am using on cygwin in the windows
> enviroment.
Any particular reason you're using software that is over four years old? There
are numerous bug fixes and performance enhancements in the 4.0.x series (with
4.0.7 being the newest).
> The command I used is: "pdb2gmx -f test.pdb -p test.top -o test.gro -ter"
> and the forcefield is Encad all- atom forcefield, using scaled down
> vacuum charges.
>
In ffencadv-c.tdb, I think there is a typo (even in the latest version of
Gromacs). Make a copy in your working directory and change the following lines
from:
[ dihedrals ]
N CA C O1
[ impropers ]
O2 CA C O1 improper_X_X_A_X
to:
[ dihedrals ]
N CA C O
[ impropers ]
OT CA C O improper_X_X_A_X
If this works, please report back and/or file a bugzilla.
-Justin
> > Date: Mon, 10 May 2010 11:00:06 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] naive question about the c-terminus
> >
> >
> >
> > abdullah ahmed wrote:
> > > I'm sorry I should have been more clear. Because the PDB file starts
> > > from residue number 23, the residue labelled 44 in the PDB is the
> > > residue that the error message refers to. Actually there is no residue
> > > 22 in the PDB file.
> > >
> > > You are also somewhat correct in saying that there are more than one
> > > chains. Currectly I am working on one chain, but the original
> structure
> > > I was working on had 10 chains (from A -J). This is why it is labelled
> > > "B".
> > >
> >
> > Then we'll need a lot more information: Gromacs version, your *exact*
> command
> > line, and what force field you're using, at least. The .pdb file
> should work
> > fine with O1 and O2; the .tdb file should rename them to O and OT,
> when adding
> > the hydrogen (HO), so I don't know why O2 is staying in place when
> impropers are
> > being added.
> >
> > -Justin
> >
> > > > Date: Mon, 10 May 2010 10:29:18 -0400
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] naive question about the c-terminus
> > > >
> > > >
> > > >
> > > > abdullah ahmed wrote:
> > > > > Hello everyone!
> > > > >
> > > > > I have a naive question and I have been trying to find a solution
> > > > > myself, but I just don't understand what is wrong.
> > > > >
> > > > > When I run pdb2gmx with "-ter" on my molecule I get the following
> > > error
> > > > > message when I ask for a COOH to be made at the C terminus (I
> get no
> > > > > error when I ask for COO- ):
> > > > >
> > > > > Atom O2 not found in residue 22 while adding improper.
> > > > >
> > > > > However, My PDB file ends with:
> > > > > ATOM 282 C LEU B 44 -5.138 -16.681 4.219 1.00 0.00
> > > > > B1 C
> > > > > ATOM 283 O1 LEU B 44 -4.407 -17.877 3.685 1.00 0.00
> > > > > B1 O
> > > > > ATOM 284 O2 LEU B 44 -6.471 -16.388 3.597 1.00 0.00
> > > > > B1 O
> > > > > TER 286 LEU B 44
> > > > >
> > > > > Therefore, the O2 atom is clearly there.
> > > > >
> > > >
> > > > The error message comes from residue 22, not 44. I'm guessing there
> > > is another
> > > > chain, for which residue 22 is the C-terminus? Likely this one is
> > > missing O2.
> > > >
> > > > > I considered the idea that the error was because there is no
> > > Hydrogen at
> > > > > the end of the PDB file to make the H in COOH. So I used ZZ
> vega to
> > > add
> > > > > a hydrogen to O2. When this did not work I tried adding one to O1,
> > > but I
> > > > > kept getting the following error:
> > > > > "Atom H1 in residue 22 not found in rtp entry with 19 atoms..."
> > > > >
> > > >
> > > > The force field expects that all of the atoms in the residue have
> > > specific
> > > > names. Adding a hydrogen should be done automatically, from the .hdb
> > > and/or
> > > > .tdb file(s).
> > > >
> > > > -Justin
> > > >
> > > > > Thank you in advance,
> > > > > Abdullah
> > > > >
> > > > >
> > >
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> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Ph.D. Candidate
> > > > ICTAS Doctoral Scholar
> > > > MILES-IGERT Trainee
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
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> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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