3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Sunipa Sarkar on November 06, 2018, 01:01:14 am

Title: do_x3dna not working
Post by: Sunipa Sarkar 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
Title: Re: do_x3dna not working
Post by: xiangjun 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 (http://forum.x3dna.org/profile/?area=showposts;u=5151), 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.

(http://docs.x3dna.org/images/set-X3DNA-env.png) and (http://docs.x3dna.org/images/update-PATH-with-X3DNA.png)

HTH,

Xiang-Jun
Title: Re: do_x3dna not working
Post by: Sunipa Sarkar 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
Title: Re: do_x3dna not working
Post by: Sunipa Sarkar 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.