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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Received on Thu May 22 2014 - 06:00:03 PDT
