AMBER Archive (2005)

Subject: RE: AMBER: ATTN REVISION

From: Junmei Wang (jwang_at_encysive.com)
Date: Wed Apr 20 2005 - 09:31:47 CDT

It seems that you have an atom type "SO" that is not in either parm99 or gaff. Is it in the ligand or your protein? If you email me your molecule, maybe I can help you.

Best

Junmei

==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang_at_encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of lv haiting
Sent: Tuesday, April 19, 2005 9:08 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: ATTN REVISION

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.
$B:_(J2005$BG/(J04$B7n(J20$BF|E*(J00:08$B!$(JJunmei Wang$B<LF;!'(J
> 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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