[gmx-users] naive question about the c-terminus

[abdullah ahmed]

The gromacs version is 3.3.1, which I am using on cygwin in the windows enviroment. 
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. 

> 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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