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: jalem...@vt.edu
> To: gmx-users@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: jalem...@vt.edu
> > > To: gmx-users@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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> > > --
> > > ========================================
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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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