R: Re: [gmx-users] numbering of .gro file

[Justin A. Lemkul]

Anna Marabotti wrote:
> Dear gmx-users,
> first let me resume my attempts on this question.
> 
> 1) Using:
> pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top
>  I obtained a .gro file in which the numbering of each chain correctly
> starts from 21 to 379 in both chains, but no chain ID is present, so I
> cannot distinguish residues of chain A from residues of chain B
> 
> 2) Using:
> pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -renum
>  I obtained a .gro file in which the numbering of each chain starts from 1
> to 359 in both chains (i.e. the second chain does not continue the numbering
> from 360), but no chain ID is present, so again I cannot distinguish
> residues of chain A from residues of chain B
> 
> 3) Using:
> pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -chainsep id
>  I obtained a .gro file in which the numbering of each chain starts from 21
> to 379 in both chains (i.e. the second chain does not continue the numbering
> from 360), but no chain ID is present, so again I cannot distinguish
> residues of chain A from residues of chain B.
> 
> 4) Using:
> pdb2gmx -f my_protein.pdb -o my_protein.pdb -p my_protein.top
>  I obtained an output .pdb file in which the numbering and the chain ID of
> the input .pdb file are kept (and so I can distinguish between the residues
> of chain A and of chain B. However, when I continue with editconf+genbox and
> add 22586 water molecules, I have the problem of more than 9999 residues,
> which is not compatible with a .pdb format, so the numbering of the residues
> restarts twice from zero.
> 
> My question is: can I distinguish chain A and B of my protein (either with a
> chain ID or with a consecutive numbering of the two chains) AND have a file
> format compatible with more than 9999 residues using Gromacs only?
> 

Probably not.  The .gro format allows for a bit more flexibility in residue 
numbering, but no chain identifiers; vice versa for .pdb.

Careful creation of index files will allow you to circumvent both problems.

-Justin

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

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

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