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

Justin A. Lemkul jalemkul at vt.edu
Mon May 10 18:08:26 CEST 2010



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: 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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-- 
========================================

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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