[gmx-developers] preserving residue numbers

[Berk Hess]

Hi,

The past years we received a lot of requests for Gromacs to preserve the 
residue numbering of the original pdb file.
Currently Gromacs simply renumbers all residues consecutively starting 
from one.
I have now implemented free residue numbering (but not committed yet), 
including pdb insertion codes.
This allows for more freedom, but therefore also some choices nedd to be 
made.

A limitation of Gromacs, which I think we would like to preserve, is 
that residue numbers are stored
per molecule type and therefore one can not have a different numbering 
in different molecules
of the same type.

My current implementation preserves the residue numbers for 
multiple-residue molecules,
but for single residue molecules (for instance water and ions) the 
residues will continue
numbering from the last residue in the last molecule before.
For a protein in water this gives the most desirable behavior. Although 
even here there are small
issues. For instance the choice of pdb2gmx writing a gro file with the 
original pdb res numbers
(e.g. for 2lzm the last prot. resnr is 164, but the first water is 166), 
which is then not what Gromacs
will produce later, because the tpr made from the top file will number 
the waters starting at 165.
Should the pdb2gmx output keep the pdb resnrs for the water or use the 
Gromacs convention?

Another effect is that for for instance polymers there will be many 
residues with resnr 1 in the system.
This is very convenient if you want to select all end groups, but less 
convenient if you want to select
a particular residue, although this can be done by selecting chains or 
molecules.

Finally several analysis tools write values as a function of residue number.
For a single protein it might be very convenient to have the original 
residue numbers in the output.
But if you have 4 chains, all with resnrs 1 to 200, things get messy.

Do you have comments or suggestions?

Berk