After completing MD the following error is showing again and again. Anyone please.
Error: Could not set up parm file prmtop for reading.
Error: Could not open parm prmtop
CPPTRAJ: Trajectory Analysis. V13.15
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Detailed description must provide.
But I guess:
You need to run the runn.in file using the following command:
cpptraj YOUR-PROTEIN-PRMTOP runn.in > runn.log
(More information could consult chapter of cpptraj in the Amber mannual)
CPPTRAJ: Trajectory Analysis. V13.15
3 ___ ___ ___ ___
4 | \/ | \/ | \/ |
5 _|_/\_|_/\_|_/\_|_
6 AmberParm Title: [default_name]
7 Radius Set: modified Bondi radii (mbondi)
8 INPUT: Reading Input from file runn.in
9 [set AMBERHOME="/opt/amber12/"]
10 [set]: Command not found.
Showing this now.
9 [set AMBERHOME="/opt/amber12/"]
10 [set]: Command not found.
A little confused... But did you read the chapter of cpptraj in amber manual or read the online tutorial (http://ambermd.org/tutorials/)?
As far as I know, the 'set' command or the [set AMBERHOME="/opt/amber12/"] is absolutely not a cpptraj command...
Please read the online resources (http://ambermd.org/tutorials/). It has a brief and step by step tutorial to perform MD simulation and cpptraj analysis.
It is better if you kindly provide the input file. I think something is wrong in your input file.
Dear Abbas,
First of all this is not an cpptraj analysis script rather it is the sander script used for running the MD simulation and hence the snapshots which you provided here is not correct.
Moreover the path given in your script is different from what is displayed in your snapshot, /public/.../Amber12 vs /opt/amber12. "9 [set AMBERHOME="/opt/amber12/"]" is different from export command.
Did you run this script which you attached here. If not please run it and provide the errors in details.
To me the script seems to be ok assuming that you have csh in your machine.
./runn.in permission denied
when running the whole simulation process this is showing after all the process.
Ok, it seems that you do not have enough permission to run the Amber. Probably you need to ask system administrator.
What we normally do is after installing the Amber in any location the path of that location is provided in the individual users .bashrc file. In that case you do not need to export it every time. Then simply run the simulation as given in AMBER tutorial.
The script you have written is also good because it reduces labor of writing all the file name every time but if you can run it without that export command, I think your problem will be solved.
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