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

[himanshu khandelia]

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
>