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)
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Received on Sat Jun 21 2014 - 09:00:02 PDT
