Hi,
I am trying to make the transition from Xplor v3.851 to pyXplor (from
Xplor-NIH-2.18.0).
To understand pyXplor I am trying to make a script which performs a
number of dynamics steps. (No complicated bussiness with restraints
besides holonomics)
I get stuck quite in the beginning. When I read the standard nucleic.par
and nucleic.top, the program complains about duplicate definitions of
parameters.
I am used to having to define
1. topology
2. parameters
3. structure (this I managed to do with protocol.loadPDB('##') )
where do I have to define steps 1 and 2 ? And how do I use multiple
parameter files ?
Sorry for this quite silly question, but I could not find it in online
documentation, FAQs, and the tutorial.
Kind regards,
Ramon van der Werf
Here is my script which I made so far:
--------------------------------------
import protocol, ivm
protocol.initRandomSeed(1)
#Define topology and subsequent parameters
protocol.initTopology('/home/ramon/COMPROG/xplor-nih-2.18/toppar/nucleic.top')
protocol.initParams('/home/ramon/COMPROG/xplor-nih-2.18/toppar/nucleic.par')
# Read PDB and generate PSF on the fly and initializes coordinates
protocol.loadPDB('par/ED_53_acc.pdb')
