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

David spoel at xray.bmc.uu.se
Wed Dec 18 07:50:00 CET 2002

On Wed, 2002-12-18 at 02:45, Senthil Kandasamy wrote:
> 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 
> number.
> 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??
The pdb standard is fuzzy. Noone ever imagined pdb files with more than
99999 atoms. I think the recommendation is to break it up into separate
files which each go up to 99999. This is bothersome too. There are no
real workarounds although pdb2gmx can handle gro and g96 files too.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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