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
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu May 22 2014 - 06:00:03 PDT
