[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 30 16:35:15 CET 2007


Your procedure sounds like it could induce an error in a number of steps.  Have
you considered simply submitting your initial .pdb file to a program like Sybyl
or DeepView and allowing it to make the mutation for you?

-Justin

Quoting himanshu khandelia <hkhandelia at gmail.com>:

> Sorry, there was a little mistake in the reported output of grompp in
> my previous email. It should be as follows:
>
> ######################
> Warning: atom names in protein.top and final.gro don't match (CD2 - HD1)
> Warning: atom names in protein.top and final.gro don't match (CE1 - CD2)
> Warning: atom names in protein.top and final.gro don't match (NE2 - CE1)
> Warning: atom names in protein.top and final.gro don't match (HE2 - NE2)
> WARNING 2 [file "protein.top", line 35]:
>   4 non-matching atom names
>   atom names from protein.top will be used
>   atom names from final.gro will be ignored
> ######################
>
> On Nov 30, 2007 3:30 PM, himanshu khandelia <hkhandelia at gmail.com> wrote:
> > Hi Folks,
> >
> > I am not being able to debug a little problem. I hope someone will be
> > able to point out the mistake. Here is what I am trying to do:
> >
> > I need to mutate a SER to a GLU residue in a protein. However, after
> > mutation (and making a new topology), when I run grompp, I get the
> > following error:
> >
> > ######################
> > processing coordinates...
> > Warning: atom names in protein.top and p.gro don't match (CD2 - HD1)
> > Warning: atom names in protein.top and p.gro don't match (CE1 - CD2)
> > Warning: atom names in protein.top and p.gro don't match (NE2 - CE1)
> > Warning: atom names in protein.top and p.gro don't match (HE2 - NE2)
> > WARNING 2 [file "protein.top", line 35]:
> >   4 non-matching atom names
> >   atom names from protein.top will be used
> >   atom names from final.gro will be ignored
> > ######################
> >
> > So, the order or names of atoms do not correspond correctly any more.
> > I cannot find out why this is the case. Here are the steps that I used
> > to make the mutation:
> >
> > ######################
> > 1. Convert the initial structure (init.gro) to a pdb (init.pdb) using
> editconf
> > 2. Pull out coordinates of the SER  from init.pdb and change residue
> > name from SER to GLU. Lets call this file residue-to-be-mutated.pdb
> > 3. Rename the following atoms: (a) OG to CG (b) HG to CD in
> > residue-to-be-mutated.pdb
> > 4. Guess remaining coordinates (for the 2 oxygen atoms on the carboxyl
> > group) in some external software
> > 5. plug in the guessed coordinates into residue-to-be-mutated.pdb
> > 6. Removed the coordinates of SER from init.pdb, and replaced them by
> > coordinates in residue-to-be-mutated.pdb. Note that because of the
> > insertion of two extra atoms, the numbering of atoms in the pdb file
> > is not continuous any more.
> > 7. Convert the resulting pdb file into .gro format using editconf.
> > Final output is final.gro, which should have continuous numbering of
> > atom numbers.
> >
> > 8. Then I also make a new protein topology using pdb2gmx.
> > ######################
> >
> > Any suggestions, anyone ?
> >
> > - The number of atoms in the initial and final .gro files differ by
> > two, which is the same as the difference in the number of atoms
> > between a SER and a GLU amino acid
> >
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========================================

Justin A. Lemkul
Graduate Research Assistant
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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