Dear Sunita ;
Why you are following such a long method taking babel. Draw your ligand or
download it from any source. Open it in Chimera. Go to DockPrep. Click the
steps. Add hydrogen add AM1-bcc CHARge. Chimera runs antechamber so you
will able to know whats your ligand charge. During running antechamber just
put nc and the charge chimera suggested thats it.
Say for example you are running antechamber in Chimera and AM1-BCC charge
showing +1 then during running put nc 1 thats easy then changing multiple
programmes.
Best;
SB
On Sat, Jun 21, 2014 at 9:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Jun 20, 2014 at 11:29 PM, sunita gupta <sunita.bio.gmail.com>
> wrote:
>
> > For atom: .R<LIG 1>.A<C1 1> Could not find vdW (or other) parameters for
> > type: C.ar
> >
>
> These are sybyl atom types, which have no associated parameters in Amber
> force fields. You should be able to convert your mol2 to one containing
> Amber/GAFF atom types using antechamber with the '-at' command line switch
> - see the manual for more details.
>
> -Dan
>
>
> > For atom: .R<LIG 1>.A<C2 2> Could not find vdW (or other) parameters for
> > type: C.ar
> > For atom: .R<LIG 1>.A<C3 3> Could not find vdW (or other) parameters for
> > type: C.ar
> > For atom: .R<LIG 1>.A<C4 4> Could not find vdW (or other) parameters for
> > type: C.ar
> > For atom: .R<LIG 1>.A<C5 5> Could not find vdW (or other) parameters for
> > type: C.ar ..... "
> >
> > Below I am attaching the .mol2 file
> >
> > Any help...
> >
> >
> > On Fri, Jun 20, 2014 at 12:32 AM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > On Fri, 2014-06-20 at 00:08 +0530, sunita gupta wrote:
> > > > Hello Everyone,
> > > >
> > > > I want to do re-scoring of many docked complexes (pdb), for which I
> > need
> > > to
> > > > make .prm and .crd files. As, it is not possible to process every
> > ligand
> > > > individually, I need any method by which I can make prep and frcmod
> > files
> > > > of all the ligands using antechamber with AM1-BCC charge method and
> > > without
> > > > specifying net chagre (-nc), as every ligand has different net
> charge.
> > >
> > > It seems you have a problem. If you want to use a QM method of any
> kind
> > > (semi-empirical, DFT, ab-initio, etc.), you need to know how many
> > > electrons you have. Ergo, you _cannot_ avoid inputting some net
> charge.
> > > You will need to find some way to determine net charge, even if it is
> > > determining the charge programmatically. Some programs in Amber are
> > > capable of chemical perception (like "reduce"), but I'm not aware of
> any
> > > that will determine net charge from an arbitrary PDB file. Of course,
> > > you also need all hydrogens to be present...
> > >
> > > > If, I am using .mol2 files, made using babel (Gastieger charge
> method),
> > > it
> > > > is giving error, and files are not made.
> > >
> > > This statement is mostly useless for anybody trying to help. We don't
> > > know what you tried [1] or what happened. Try to put yourself in our
> > > shoes and isolate the problem. We need enough information to reproduce
> > > or understand what went wrong but not so much information that we can't
> > > justify spending the time to wade through irrelevant details.
> > >
> > > Good luck,
> > > Jason
> > >
> > > [1] Paraphrasing or describing in words what you tried is not helpful.
> > > What people thought they did or tried to do is often different from
> what
> > > they _actually_ did -- only the exact commands, scripts, etc. that you
> > > used (along with the exact output) will tell us what you _actually_ did
> > > and let us help.
> > >
> > > When the description of the problem is vague, the root cause could be
> > > _anything_ -- user error or program bug. We (developers of any
> program,
> > > really) will assume the former until we can be reasonably convinced
> that
> > > the latter is true.
> > >
> > > --
> > > Jason M. Swails
> > > BioMaPS,
> > > Rutgers University
> > > Postdoctoral Researcher
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > --
> > SUNITA GUPTA
> > Senior Research Fellow
> > Bioinformatics Centre
> > Jawaharlal Nehru University
> > New Delhi- 110067
> > Email- sunita.bio.gmail.com
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Sun Jun 22 2014 - 07:00:02 PDT
