See a tutorial is cool there is no doubt. Just a co-relation all developers
test when they implement something. Thats the part developers know better
than users. Now there come common problem which people face. To make it
updated and more towards problem solving the common problems in each case
it may be in tleap or may be in any other steps should be there in the
tutorial in an interactive question answer basis or with another tutorial
named " Common Errors; Debugs and All".
Say for example there is common problem for which people asked much in the
mailing list " one common problem is <FATAL> during running tleap". So the
beneficial part of adding common problems during running as a separate
tutorial or as a note will make it more user friendly than searching
different threads by GOOGlE.
Best
S.B
On Thu, May 22, 2014 at 3:49 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Bhakat,
>
> Unfortunately making tutorials for all the possible combinations of
> options would be impossible. We struggle to keep the tutorials up to date
> as they are. In terms of what level of QM theory to use this is a research
> question in itself and way beyond the scope of tutorials which are simply
> designed to show how to use a particular method. I suggest looking at the
> literature and consulting with some of the authors so you can make an
> informed decision on what level of theory to use.
>
> I also not that 'qmtheory' - without the underscore has been deprecated.
> Take a look at the SQM and the QMMM sections of the AMBER 14 manual and
> read it thoroughly. Note the variable that one is supposed to use these
> days is qm_theory. In your case you would set qm_theory='DFTB'
>
> Probably the tutorial should be updated. Volunteers please? Perhaps when
> people update the manual they could take the time to update the tutorials
> for the section of code they are responsible for?
>
> All the best
> Ross
>
>
>
> On 5/22/14, 5:49 AM, "Soumendranath Bhakat"
> <bhakatsoumendranath.gmail.com> wrote:
>
> >Just a request, I noticed that there is no details of Amber tutorial on
> >hybrid QM/MM method expect only one tutorial. Some components like what
> >qmtheory will be used for what level of Qm is also not there. Say for
> >example I use a DFTB-SCC level I will give qmtheory=7 so many people might
> >use some other QM level but it is not in that tutorial.
> >
> >Also the QM/MM tutorial is no that much developed compared to other
> >tutorials. This discussion is nice one. Will it be possible to update the
> >QM/MM tutorial with new updates mentioning possible errors and other
> >necessary points.
> >
> >All d best!!
> >
> >
> >On Thu, May 22, 2014 at 2:42 PM, James Starlight
> ><jmsstarlight.gmail.com>wrote:
> >
> >> Jason,
> >>
> >>
> >> many many thanks!
> >>
> >> James
> >>
> >>
> >> 2014-05-22 16:34 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> >>
> >> > On Thu, 2014-05-22 at 16:10 +0400, James Starlight wrote:
> >> > > Hi Jason,
> >> > >
> >> > > Please provide me with a few examples (I didnt find it in the
> >>manual or
> >> > in
> >> > > the help of tleap):
> >> > > for instance I need to calculate charge of resname CRQ which is the
> >> part
> >> > of
> >> > > the "chimera" unit.
> >> >
> >> > charge chimera.CRO
> >> >
> >> > > Alternatively I need to calculate total charge of residues 20-23
> >>which
> >> is
> >> > > the part of the same unit.
> >> >
> >> > charge chimera.20
> >> > charge chimera.21
> >> > charge chimera.22
> >> > charge chimera.23
> >> >
> >> > and add them together. tleap also has a command "desc" (for
> >>'describe')
> >> > that will print out details about a particular unit or container. For
> >> > example, the command "desc GLU" returns the following output:
> >> >
> >> > > desc GLU
> >> > UNIT name: GLU
> >> > Head atom: .R<GLU 1>.A<N 1>
> >> > Tail atom: .R<GLU 1>.A<C 14>
> >> > Contents:
> >> > R<GLU 1>
> >> >
> >> > telling you there is 1 residue named GLU (and you can access items in
> >>a
> >> > container with either their name if that name is unique or their
> >> > number). If you want to investigate the contents of the GLU residue
> >>of
> >> > the GLU container, the command "desc GLU.GLU" or "desc GLU.1" prints
> >>the
> >> > following:
> >> >
> >> > > desc GLU.GLU
> >> > RESIDUE name: GLU
> >> > RESIDUE sequence number: 1
> >> > RESIDUE PDB sequence number: 0
> >> > Type: protein
> >> > Connection atoms:
> >> > Connect atom 0: A<N 1>
> >> > Connect atom 1: A<C 14>
> >> > Improper torsions:
> >> > Contents:
> >> > A<N 1>
> >> > A<H 2>
> >> > A<CA 3>
> >> > A<HA 4>
> >> > A<CB 5>
> >> > A<HB2 6>
> >> > A<HB3 7>
> >> > A<CG 8>
> >> > A<HG2 9>
> >> > A<HG3 10>
> >> > A<CD 11>
> >> > A<OE1 12>
> >> > A<OE2 13>
> >> > A<C 14>
> >> > A<O 15>
> >> >
> >> > Likewise, you can get information about a particular atom by accessing
> >> > the atom name (or number) of that residue:
> >> >
> >> > > desc GLU.1.N
> >> > ATOM
> >> > Normal Perturbed
> >> > Name: N N
> >> > Type: N N
> >> > Charge: -0.5163 0.000
> >> > Polarization: 0.0000 0.000
> >> > Element: N (not affected by pert)
> >> > Atom flags: (decimal 131072 hex 0x20000)
> >> > posfxd n posblt n posdrwn n selected n
> >> > pert n notdisp n touched n posknwn Y
> >> > internal n needsmin n needsbuild n
> >> > Atom position: 3.325770, 1.547909, -0.000002
> >> > Atom velocity: 0.000000, 0.000000, 0.000000
> >> > Bonded to .R<GLU 1>.A<H 2> by a single bond.
> >> > Bonded to .R<GLU 1>.A<CA 3> by a single bond.
> >> >
> >> >
> >> > One of these days maybe an "advanced" tleap tutorial will be
> >>created...
> >> >
> >> > Also, if you want to compute the charge of a selection, you can load
> >>the
> >> > topology file into parmed.py and use the "netCharge" command to print
> >> > out the net charge of a particular atom mask. So something like:
> >> >
> >> > parmed.py -p your.prmtop << EOF
> >> > netCharge :20-23
> >> > EOF
> >> >
> >> > Hope this helps,
> >> > Jason
> >> >
> >> > --
> >> > Jason M. Swails
> >> > BioMaPS,
> >> > Rutgers University
> >> > Postdoctoral Researcher
> >> >
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> >--
> >Thanks & Regards;
> >Soumendranath Bhakat
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu May 22 2014 - 07:30:03 PDT
