Hello,
You may first run antechamber to get prepi file assigning gaff atom
types. Then you load amber force field (leaprc.ff99, leaprc.ff94 ...)
and gaff (leaprc.gaff) as well as the generated prepi file to leap.
Then, load pdb file, add solvent ... and save topology file. Hopefully,
this procedure works for you.
All the best
Junmei
Thanks! The ligand is sildenafil. When I use:
antechamber -i sid.out -fi gout -o sid.prep -fo prepi -c resp
and
parmchk -i sid.prep -f prepi -o sid.frcmod
There is not any ATTN REVISION information in the sid.frcmod
file. But When I load the parameters to my PDB file, the system always
tell me there is one unknown element. So I have to use the fllowing
order:
antechamber -i sid.out -fi gout -o sid.prep -fo prepi -c resp
-at amber
and
parmchk -i sid.prep -f prepi -o sid.frcmod
This time there is many ATTN REVISION in the sid frcmod. Such
as:
SO 0.000 0.000 ATTN, need revision
CA-SO 0.00 0.000 ATTN, need revision
SO-O 0.00 0.000 ATTN, need revision
SO-NT 0.00 0.000 ATTN, need revision
CA-SO-O 0.000 0.000 ATTN, need revision
CA-SO-NT 0.000 0.000 ATTN, need revision
SO-NT-CT 0.000 0.000 ATTN, need revision
O -SO-O 0.000 0.000 ATTN, need revision
O -SO-NT 0.000 0.000 ATTN, need revision
CA-SO-NT-CT 1 0.000 0.000 0.000 ATTN, need revision
SO-NT-CT-H1 1 0.000 0.000 0.000 ATTN, need revision
SO-NT-CT-CT 1 0.000 0.000 0.000 ATTN, need revision
O -SO-NT-CT 1 0.000 0.000 0.000 ATTN, need revision
Thanks for your help!
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Received on Tue Apr 19 2005 - 17:53:01 PDT
