[gmx-users] mapping indices in posre/topol files to those in index files

[Irem Altan]

Hi,

I have .pdb file that contains of three copies of a protein with two chains each. For convenience I had named both chains of each copy identically. I therefore have a .pdb file that looks like this:

ATOM … A …
….
ATOM … A …
TER
ATOM … A …
….
ATOM … A …
TER
ATOM … B …
….
ATOM … B …
TER
ATOM … B …
….
ATOM … B …
TER
ATOM … C …
….
ATOM … C …
TER
ATOM … C …
….
ATOM … C …
TER

When I do pdb2gmx, this produces the following topol files:

topol_Protein_chain_A.itp
topol_Protein_chain_A2.itp
topol_Protein_chain_B.itp
topol_Protein_chain_B2.itp
topol_Protein_chain_C.itp
topol_Protein_chain_C2.itp

(the posre_* files are named similarly). 

The indices of atoms in these files always start from 1. However, when I create an index file, the indices are such that all atoms are numbered from 1 to the total number of atoms in the system. Therefore atom #1 in a topol file maps to some other number in the index file. The question is, in what order the atoms are counted? After the last atom of chain_A, do I continue with the first atom of chain_A2, etc.?

Best,
Irem