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

[Justin A. Lemkul]

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
>  > >
>  > > 
> ------------------------------------------------------------------------
>  > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign
>  > > up now. <https://signup.live.com/signup.aspx?id=60969>
>  > >
>  >
>  > --
>  > ========================================
>  >
>  > 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
>  >
>  > ========================================
>  > --
>  > gmx-users mailing list gmx-users at gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at http://www.gromacs.org/search before 
> posting!
>  > Please don't post (un)subscribe requests to the list. Use the
>  > www interface or send it to gmx-users-request at gromacs.org.
>  > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> ------------------------------------------------------------------------
> Hotmail: Powerful Free email with security by Microsoft. Get it now. 
> <https://signup.live.com/signup.aspx?id=60969>
> 

-- 
========================================

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

========================================