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