Hi all,
I have a pyrophosphate residue in my protein pdb. According to J Comp Chem
2003, 24, 1016-1025 I need to create a new atom type O3. So in
the /usr/local/amber11/dat/leap/cmd/leaprc.ff99SB I added the new atom type
as
{ "O3" "O" "sp2" }
and then in the /usr/local/amber11/dat/leap/parm/parm99.dat I made the
necessary changes for mass, bond,angle,torsions.
Now when I do
parmchk -i pop.prep -f prepi -o pop.frcmod
Still the pop.frcmod says
O3 0.000 0.000 ATTN, need revision
O3-P 0.00 0.000 ATTN, need revision
O3-P -O3 0.000 0.000 ATTN, need revision
O3-P -OS 0.000 0.000 ATTN, need revision
O3-P -OS-P 1 0.000 0.000 0.000 ATTN, need
revision
Could any one please tell me why parmchk doesn't recognize the newly
updated values for O3 atomtype or advise me if I have overlooked something?
Thank you very much
Sajeewa Dewage
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Received on Fri Oct 18 2013 - 06:30:03 PDT
