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.
Mark
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