Bash script for making complexes of ligands and receptor
I am working with autodock vina for virtual screening and docking with cygwin. Autodock vina generates conformers for multiple ligands. I want to make the complex of these conformers with receptor. e.g. I have 100 .pdbqt files form vina output and one receptor pdbqt file. By running command-
I can convert inh*.pdbqt to pdb, but I have to do this individually for all ligands (* here are random numbers from pubchem database).
With command-
With this command the pdb of complex of receptor and ligand is generated, but again this I have to do for each ligand, receptor file is fixed in this case.
I want a bash script for above to commands to run in cygwin. Aim is to use multiple ligand files - convert them to pdb - merge with receptor.pdbqt - generate multiple complexes as per ligand names.
This may need a simple script. Though I have worked with many scripts I don't know how to write such bash scripts. Naively, I have given a try and wrote one script-
It generates the complex but only one complex with all ligands in it !!!
Last edited by Scrutinizer; 01-18-2015 at 04:05 AM..
Reason: code tags
Hi All,
I am trying to monitor CPU load of few processes, with the same name.
The output that I get from top is the following
28171 root 20 0 1089m 21m 3608 S 103 0.3 15:16.89 /opt/ppp//h264rtptranscoder.bin --videoPort=14504 --audioPort=14505
27589 root 20 0 1060m 23m... (3 Replies)
Here's the assignment. I'll bold the parts that are rough for me. Unfortunately, that's quite a bit lol. The syntax is, of course, where my issues lie, for the most part. I don't have a lot of programming experience at all :/. I'd post what I've already done, but I'm so lost I really don't know... (1 Reply)
Hello all!
This is my first post and I'm very new to programming. I would like help creating a simple perl or bash script that I will be using in my work as a junior bioinformatician.
Essentially, I would like to take a tab-delimted or .csv text with 3 columns and write them to a "3D" matrix:
... (16 Replies)
ok basically im trying to count how many people fail a class by comparing there grade by -gt 49
i tried putting a count inside the while loop but i know you cant access a count outside a subshell. is there an easy way to count the number of failures?
declare -i failcount=0
awk... (2 Replies)
First let me explain the scenario
I have tywo files as usual
file1.txt (it has n rows and 8 columns)
$1 $2 $3 $4 $5 $6 $7 $8
Code:
1234567|iufgt|iuoy|iout|white |black |red |90879
1234567|iufgt|iuoy|iout|green |pink |blue |90879... (3 Replies)
Hello everyone!I am trying to make a mail list(a simple .txt file)in which i put certain records that match specific criteria.
Let's say that i have a(sorted by last column file)like this one:
0100567 Bla1 Lala1 100
1234567 Bla2 Lala2 80
8769029 Bla3 Lala3 70
1001007 ... (0 Replies)
Hello once again:
One thing that seems to be a nice feature is a progress gauge... so I can see how long an operation will take for a task to complete if it is requiring a lot of processing or the file is enormous. I have seen references to gauge operations, but I don't know anything about it or... (1 Reply)
I'm using Mac OSX.
And i want to make an visual application based on bash command.
But, apple script doesn't support Terminal command.
So please tell me how to turn my dream into a reality. :o
I mean purely by bash! (0 Replies)