[Dock-fans] install question

Trent E. Balius tbalius at aol.com
Sun Sep 25 06:33:47 PDT 2016


Hi Haiyang, 

I think that you are save in proceeding with docking unless you want to do something specific (using the multi-grid footprinting scoring function). 

It looks like the problem maybe because of this line: 
 `grep -A 1 range_union important_residues.out | sed -e'/range_union/d' -e'/--/d' -e's/ //g' | tr ',' '\n' | sort -nu`

This command will return a list of residues.

The back quotes mean, in csh, to convert what this command returns to text. 

Try switching the shell, just type the following on the command line:

> echo $SHELL # this will tell you what shell you are using
> csh # this will open up a cshell session
> make test
> exit # this will close the cshell session and return to the your old environment


Questions to consider: 
Is this because you are using bash instead of csh? 
( if this is the case, we may consider modifying this test to not depend on the shell for a future release.)
Does the above line work when you run it on the command line?
Is it do to not having grep or sed installed or in your path? 
On what environment are you running dock? 

I hope that this helps,

Trent


 

 

======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: 钟海洋 <zhonghy14 at lzu.edu.cn>
To: Trent E. Balius <tbalius at aol.com>
Sent: Fri, Sep 2, 2016 6:47 pm
Subject: Re: Re: [Dock-fans] install question


Hi Trent,


Thank you very much first. I have installed python and the version is 2.7.12 and the error is still here. What should I 


do to solve this problem ? Thanks.


Haiyang





-----原始邮件-----
发件人:"Trent E. Balius" <tbalius at aol.com>
发送时间:2016-09-02 23:14:30 (星期五)
收件人: zhonghy14 at lzu.edu.cn, dock-fans at docking.org
抄送: 
主题: Re: [Dock-fans] install question

Hi Haiyang, 


This "make test" is testing that everything has been installed correctly.   

 If this is your only error and you want to do normal docking, you may proceed with docking.

However, If you want to use the multigrid-footprint scoring function, then you should try and resolve this.

This error may indicate that you do not have python installed on your machine, try installing python. 

I hope this helps,

Trent

 

======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: 钟海洋 <zhonghy14 at lzu.edu.cn>
To: dock-fans <dock-fans at docking.org>
Sent: Fri, Sep 2, 2016 6:59 am
Subject: [Dock-fans] install question

Hi guys,

       I got this error message during the step 5 of installation (make test):

../../../bin/multigrid_fp_gen.py rec.mol2 resid grid.in `grep -A 1 range_union important_residues.out | sed -e'/range_union/d' -e'/--/d' -e's/ //g' | tr ',' '\n' | sort -nu`
/bin/sh: ../../../bin/multigrid_fp_gen.py: /usr/bin/python: bad interpreter: Permission denied
make[2]: *** [fps_grids] Error 126

       how to solve it and install dock6.7 correctly? I need your help.
      
                                                                  thanks
                                                                         Haiyang
_______________________________________________
Dock-fans mailing list
Dock-fans at docking.org
http://mailman.docking.org/mailman/listinfo/dock-fans





-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20160925/6d704d37/attachment.html 


More information about the Dock-fans mailing list