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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Received on Mon Aug 12 2019 - 08:00:02 PDT
