[gmx-users] editconf truncates the residue number to four digits in pdb files

Senthil Kandasamy senthilk at engin.umich.edu
Wed Dec 18 02:45:42 CET 2002

I have a reasonably large system. (~60000 atoms with >35,000 waters).
So there are more than 10,000 waters.
When I use editconf to manipulate and create pdb files, it truncates the 
fifth column of the pdb file ,
which is the residue number, to four digits.
Hence, for the 30,001st SOL atom, I get  a residue number of 1, (the 
same residue number as SOL 1).
This basically means that two different molecules have the same residue 
I use these pdb files to sort out atoms and this problem of "multiple 
molecules with same residue number"
 throws a big wrench into my algorithm and analysis. Is there a work 
around for this problem?
The gro files are okay, but I really need the correctly formated pdb 
files to get this working.

Is this something that editconf overlooks or is that the way pdb files 
are standardized??

I have been trying to debug my (correct) code without realizing that the 
pdb files were not what I thought they would be.


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