AMBER Archive (2005)

Subject: Re: AMBER: ATTN REVISION

From: lv haiting (lhaiting_at_126.com)
Date: Tue Apr 19 2005 - 21:08:14 CDT

Hello,
    Yes, I did the same progress as the same as what you said. I first
run antechamer:
    antechamber -i sid.out -fi gout -o sid.prep -fo prepi -c resp
So I get prepi file assigning gaff atom types. Then I run parmchk:
    parmchk -i sid.prep -f prepi -o sid.frcmod

Then I load amber force field (leaprc.ff99):
    tleap -s -f leaprc.ff99
    mod=loadamberparams sid.frcmod
    loadamberprep sid.prep
    source leaprc.gaff
    RL=loadpdb file.pdb
At this here, when I load the pdb file, the system tell me that there is
one unkown element. Why? When I delete the ligand molecule and only load
the protein molecule, there is not unknown element cue. So the problem
should be at the ligand molecule.
    Thanks!

Do the unknown element affect on my result.
在2005年04月20日的00:08，Junmei Wang写道：
> 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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