[gmx-users] Regarding numbering

P.R.Anand Narayanan nandu_cooldevil at yahoo.co.in
Fri Jul 10 12:37:54 CEST 2009

Dear gromacs users,
my protein has 4453 atoms and 583 residues. after running the pdb2gmx command it got converted to 5657 atoms and 581 residues. I cut and pasted the HETATMS from the initial pdb file into a separate file.
My queries are:
1. how did the number of atoms and residues change.
2. while pasting the HETATMS of the cofactors and the related molecules necessary in the newly created pdb file (from that separate file), I changed the changed the number of atoms accordingly (that is numbers starting from 4454 to numbers starting from 5658). My question is that whether i should change the numbers of the residues also accordingly???? since the numbering of residues of cofactors and other necessary molecules werent in the sequentially ordered number.....
Please help...........

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