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Author Topic: do_x3dna not working  (Read 4853 times)

Offline Sunipa Sarkar

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do_x3dna not working
« on: November 06, 2018, 01:01:14 am »
Hii
 I have installed do_x3dna and 3DNA package successfully. I can access 3DNA package by giving command find_pair or analyze. But when I am trying to execute do_x3dna for a trajectory file, I am getting the following fatal error:
  Failed to execute command: $X3DNA/bin/analyze ddUJotW7.inp
 Can you please help me with this? I have followed the installation procedure discussed in the forum
 http://forum.x3dna.org/howtos/how-to-install-3dna-on-linux-and-windows/. I have one doubt which is mentioned there "set the environment variable X3DNA and add $X3DNA/bin to your command search path ": add $X3DNA/bin to your command search path what does that mean? Please explain.

Thanks

Offline xiangjun

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Re: do_x3dna not working
« Reply #1 on: November 06, 2018, 10:28:25 am »
Thanks for using 3DNA and for posting your questions on the Forum.

There are two parts to your questions, related to 3DNA per se, and do_x3dna on top of it. You have installed 3DNA successfully since you can access find_pair or analyze. I am not sure you have installed do_x3dna correctly since you cannot run it on a trajectory file. Rajendra Kumar, the developer of do_x3dna, may be available to answer your questions on the Forum. Or you may directly contact him for help.

As to "set the environment variable X3DNA and add $X3DNA/bin to your command search path", the post you referred to has explained it all -- pay close attention to steps 4.4 and 4.5 which has annotated screenshots (see the links below). If that does not help, please consult a local, experienced Windows user.

and

HTH,

Xiang-Jun
« Last Edit: November 06, 2018, 12:16:00 pm by xiangjun »

Offline Sunipa Sarkar

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Re: do_x3dna not working
« Reply #2 on: November 07, 2018, 04:13:05 am »
Hello
Thank you for your suggestion. I am using a linux machine and trying to install the software there. Sorry I have not mentioned in the previous post. Actually I am trying to ensure whether the error is coming because of the 3DNA package installation or do_x3dna installation. Becuase I can access both the softwares. But when I am trying to analyze a trajectory file then this fatal error is coming. Should I install bothe the softwares in same path? I have install both the softwares in different paths and I have modified my bashrc file according to that.
.bashrc file:

export X3DNA='/home/prashant/software/x3dna-v2.3'
export PATH='/home/prashant/software/x3dna-v2.3/bin':$PATH
export PATH=$PATH:$X3DNA/bin
export do_x3dna='/usr/local/do_x3dna'
export PATH='/usr/local/do_x3dna/bin':$PATH

Please correct me. If this a problem regarding do_x3dna installation then I will contact Mr. Rajendra Kumar.
Thanks

Offline Sunipa Sarkar

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Re: do_x3dna not working
« Reply #3 on: November 07, 2018, 10:09:15 am »
Hello Xiang
I have solved the problem by contacting Mr. Rajendra kumar. It was a problem of  PBC correction of my trajectory.
Thank you for the suggestion.

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.