[gmx-users] pdb files using hex resid

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 4 02:46:09 CET 2012

On 4/01/2012 12:30 PM, Peter C. Lai wrote:
> I used VMD to process a gro file and wrote it to pdb, because VMD can't
> write gro files.  Because the # of residues exceeds 9999, it numbered the
> remaining residues in the PDB in 4 bit hex. Editconf will not convert the
> hex numbered residue ids back to decimal (it just truncates anything past
> the final 0-9 digit in the field). Does this mean if I feed the pdb as-is
> into grompp it will also have problems reading the residue numbers?
> Gromacs 4.5.3

Yes. VMD is writing non-standard-compliant PDB. Blame it.

If you've linked GROMACS to the dlopen library from VMD (the default) 
then GROMACS can read whatever VMD writes, so pick a useful format.


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