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.
Mark
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