> It seems like the cpptraj numbering starting from 1 is the correct one
but I want to double check.
I might be wrong but I think in AMBER interface, the index is 1-based.
In pytraj, if the return value is *not* string, the index is 0-based.
> pt.select_atoms(':1', ...)
In this case, the return value is a list of int with 0-based, and the
residue selection follow AMBER's selection syntax (1-based).
cheers.
Hai
On Mon, Aug 12, 2019 at 10:38 AM Rosellen, Martin <
martin.rosellen.16.ucl.ac.uk> wrote:
> Dear Amber Users,
>
> I am writing a script to automate the set up of configuration files for
> umbrella sampling runs. I figured that cpptraj uses different atom
> numbering than pytraj:
>
> CPPTRAJ: Trajectory Analysis. V18.01
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 08/12/19 15:24:53
> | Available memory: 11.825 GB
>
> Loading previous history from log 'cpptraj.log'
> > parm WT.prmtop
> [parm WT.prmtop]
> Reading 'WT.prmtop' as Amber Topology
> Radius Set: H(N)-modified Bondi radii (mbondi2)
> > trajin WT.inpcrd
> [trajin WT.inpcrd]
> Reading 'WT.inpcrd' as Amber Restart
> > select :1
> [select :1]
> Selected 21 atoms.
> Selected= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
>
>
> Python 3.7.3 (default, Mar 27 2019, 16:54:48)
> [Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import pytraj as pt
> >>> pdb = pt.load('WT.inpcrd','WT.prmtop')
> >>> print(pt.select_atoms(':1', pdb.top<http://pdb.top>))
> [ 0 1 2 ... 18 19 20]
>
> What numbering should I use in the umbrella restraint files? I mean the
> ones that look like this:
>
> Harmonic restraints for 120 deg
> &rst
> iat=9,15,17,19,
> r1=-60.0, r2=120.0, r3=120.0, r4=300.0,
> rk2=200.0, rk3=200.0,
> /
>
> It seems like the cpptraj numbering starting from 1 is the correct one but
> I want to double check.
>
> cheers
> Martin
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>
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Received on Mon Aug 12 2019 - 08:00:03 PDT
