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 - 06:00:02 PDT
