And also rescoring of all docked poses using MM/GBSA is not good until it
is showing good IC50. You can dock or screen as much as you can and rscore
top 10 compounds with MM/GBSA or even more appropiately QM/MM/GBSA approach.
On Sun, Jun 22, 2014 at 7:04 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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
>
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Sun Jun 22 2014 - 07:00:03 PDT
