[gmx-users] virtual site error

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 12 18:28:16 CET 2010

On 12/11/2010 5:01 AM, Ting Zhou wrote:
> Hi,
> when I run
> pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p
> -vsite hydrogens -ignh ,
> I got
> Fatal error:
> Invalid directive HISD in vsite database
> /home/XXX/gromacs/g/share/gromacs/top/oplsaa.ff/aminoacids.vsd .
> What is the problem? 2KO3.pdb was downloaded from PDB.

What GROMACS version?

src/kernel/gen_vsite.c is buggy. There are hardcoded mentions of "HID" 
and "HISA", but not of "HISD" (which is well-formed for OPLS/AA). I am 
not sure what the fix is. Please file a bugzilla report.


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