[gmx-users] naive question about the c-terminus
abdullah_renk_ahmed at hotmail.com
Mon May 10 16:50:06 CEST 2010
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".
> 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).
> > Thank you in advance,
> > Abdullah
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
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> Department of Biochemistry
> Virginia Tech
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