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: [email protected]
> To: [email protected]
> 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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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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