AMBER Archive (2005)

Subject: AMBER: Re: antechamber not working .. for thio residue..

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Fri May 20 2005 - 04:32:19 CDT

to all amber users,

I have done as advices by Jenk,
but when I use antechamber I get the message as below:

the command I used is :

antechamber -i thio.pdb -fi pdb -o thio.thio1 -fo
thio1 -at
gaff -c bcc -nc 0 -rn MOL -j 5

Running: /usr/local/amber7/exe/mopac.sh
ANTECHAMBER_MUL.MOP ANTECHAMBER_MUL.OUT
/usr/local/amber7/exe/mopac.sh: line 11:
/usr/local/amber7/exe/mopac: No such fi
                           le or directory
Unable to find mopac charges in ANTECHAMBER_MUL.OUT

What is the meaning of this message and how to over
come this.

Thank you.
Vijay
--- Cenk Andac <cenk_andac_at_yahoo.com> wrote:

> Your molecule does not seem as complex.
> All bond, angle, torsion and improper torsion
> parameters are available in the GAFF library at
>
> $AMBERHOME/amber8/dat/leap/parm/gaff.dat
>
> Construct and pre-minimize your molecule in leap.
> save the molecule in pdb format in leap as mol.pdb.
> (i.e.; savepdb mol mol.pdb)
> Exit leap.
>
>
> Now, you need to convert your pdb file to a mol2
> file
> by antechamber.
>
> Assuming that your molecule has zero net charge,
> run antechamber as
>
> $AMBERHOME/exe/antechamber -i mol.pdb -fi pdb -o
> mol.mol2 -fo mol2 -at gaff -c bcc -nc 0 -rn MOL -j 5
>
>
> ..takes about a couple of minutes.
>
> After the antechamber job is done, take a close look
> at the mol.mol2 file in the current directory. Note
> that atom types are recorded in lowercase, and also
> you should have AM1-BCC partial atomic charges in
> the
> mol2 file ready for energy computations.
>
> Re-execute leap
> load in the GAFF library as
>
> source leaprc.gaff
>
> load in your mol2 molecule in leap as
>
> mol=loadmol2 mol.mol2
>
> create prmtop and x files as
>
> saveamberparm mol mol.prmtop mol.x
>
> quit
>
>
> hope this works for you..
>
> jenk..
> --- Vijay Manickam Achari <vjrajamany_at_yahoo.com>
> wrote:
> > Dear amber users, when I tried to use
> > saveamberparms,
> > I get the output as below.
> >
> >
> > > saveamberparm thio thio.top thio.crd
> > Checking Unit
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Could not find bond paramter for: CG - S
> > Building angle parameters.
> > Could not find angle parameter: H2 - CG - S
> > Could not find angle parameter: CG - S - CT
> > Could not find angle parameter: OS - CG - S
> > Could not find angle parameter: CG - CG - S
> > Building proper torsion parameters.
> > * * No torsion terms for H2-CG-S-CT
> > * * No torsion terms for OS-CG-S-CT
> > * * No torsion terms for CG-OS-CG-S
> > * * No torsion terms for H1-CG-CG-S
> > * * No torsion terms for CG-CG-S-CT
> > * * No torsion terms for OH-CG-CG-S
> > Building improper torsion parameter.
> > old PREP-specified impropers:
> > total 0 improper torsions applied
> > 0 improper torsions in old prep form
> > Building H-Bond paramters
> > Parameter file was not saved.
> >
> >
> > --- Ilyas Yildirim <yildirim_at_pas.rochester.edu>
> > wrote:
> > > Hi Vijay,
> > >
> > > Can u copy/paste the error message u are
> getting?
> > > And also the residue
> > > that u have created in xleap. I would guess that
> > you
> > > need to define
> > > the improper torsion angles in your modified
> > frcmod
> > > file in order xleap
> > > to understand the new structure.
> > >
> > > On Thu, 19 May 2005, Vijay Manickam Achari
> wrote:
> > >
> > > > Hi to all amber users,
> > > > I am attempting to model micelle sturcture
> with
> > > using
> > > > thio-beta-octyl-D-glucopyranoside residue.
> > > > For that I tried to model a single residue of
> > > > thio-beta-octyl-glucopyranoside using xleap
> > > editor.
> > > > I have also changed to atom type for sulfur S.
> > > >
> > > > After model I tried to save the single residue
> > > using
> > > > SAVEAMBERPARM command.
> > > > But it failed to save.
> > > > It says improper torsion angles.....
> > > > S-CT-...
> > > > CT-S....
> > > >
> > > > How I should solve this problem?
> > > > Where do I can get the parameter for sulfur
> and
> > > > glucopyranoside head of sugar? (because the
> > sulfur
> > > > atom is linking atom between head and tail of
> > the
> > > > atom)
> > > >
> > > > What should I do to overcome this error?
> > > >
> > > > Can any one there help me?
> > > > Thank you very much
> > > > With high hope.
> > > > Vijay Manickam Achari

        
        
                
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