You nearly had it! You didn't put a ; or newline before the 'do', though.
You don't need to put the filenames in a variable. That could actually be bad -- $FILES will split "file name.pdbgt file2.pdbgt" into "file", "name.pdbgt", "file2.pdbgt". "for FILE in *" won't.
You also don't need to put the ".pdbgt" back on the end, it never left
This code is in my 'case' statement and it all else works fine.
The problem I have is that the value in 'procno' is not passed on to the external program (fireit).
It is passing all zeros instead of the actual process number.
By the time I get to this case statement, I know the "Number" and... (1 Reply)
Hi,
I have a program in /opt/local/bin, my path in my .profile is
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
however when i type the program name it cannot find it, however i know the program is in /opt/local/bin?
Thanks (2 Replies)
Hello
I am getting error when the file (Folder or Application) path having space is given as external input to the shell program.
It works fine for the files which has no spaces in the file name
Thans, (5 Replies)
Hello,
in the application i'm writing i need to launch "recordmydesktop" to capture the screen,but i'm having a problem: when the recording stops,and the encoding of the saved file starts,the entire system hangs until the completion of the encoding.This happens if i launch recordmydesktop from my... (7 Replies)
Hi,
in my program i need to run an external program in background.I am aware that there are at least 2 alternatives for this:
1)fork+exec
2)system("program &");
I have read several posts about this,and they all tend to suggest to use fork+exec (and that's what i am doing now).
I have some... (2 Replies)
Sorry for such a dreadful title, but I'm not sure how to be more descriptive. I'm hoping some of the more gurutastic out there can take a look at a solution I came up with to a problem, and advice if there are better ways to have gone about it.
To make a long story short around 20K pieces of... (2 Replies)
I have asked this before but I haven't had any luck so far getting this to work. I use RCS(revision control system). When it runs if I pass the value 'unlock' to $3 its reassigned to $unlock. When I run the command (rcs -u'version number' 'filename') ti will ask me 1-(Do you want to break the lock... (5 Replies)
Hi all,
I am using an external binary to view memory starting from a specific address and i want to automate this via PERL however there are problems. Hope you can help me ..thx
The output of the programme is like below:
bash-3.2$ mem_disp 12B21D20 100
Opening RO Data Memory File scp.ro... (4 Replies)
Hi,
I have created a Shell Script and invoke through java using Process Builder
It's working fine, if (Shell script file ) in the same directory as java file.
By Problem:
How to run the Shell Script file( resides in external directory) using java. What configuration i have... (1 Reply)
Dear community,
I communicate with an external program (maxima) using named pipes. If I use a text file to capture the output (maxima > out.txt) i can see the programs answer directly after the input written into the file. But if bypass the output into a named pipe (maxima > pipe) and capture it... (1 Reply)
Discussion started by: Pustekuchen
1 Replies
LEARN ABOUT DEBIAN
vina
AUTODOCK(1) General Commands Manual AUTODOCK(1)NAME
vina - docking small molecules against proteins
DESCRIPTION
Input:
--receptor arg
rigid part of the receptor (PDBQT)
--flex arg
flexible side chains, if any (PDBQT)
--ligand arg
ligand (PDBQT)
Search space (required):
--center_x arg
X coordinate of the center
--center_y arg
Y coordinate of the center
--center_z arg
Z coordinate of the center
--size_x arg
size in the X dimension (Angstroms)
--size_y arg
size in the Y dimension (Angstroms)
--size_z arg
size in the Z dimension (Angstroms)
Output (optional):
--out arg
output models (PDBQT), the default is chosen based on the ligand file name
--log arg
optionally, write log file
Misc (optional):
--cpu arg
the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)
--seed arg
explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9)
maximum number of binding modes to generate
--energy_range arg (=3)
maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)
Configuration file (optional):
--config arg
the above options can be put here
Information (optional):
--help display usage summary
--help_advanced
display usage summary with advanced options
--version
display program version
SEE ALSO
AutoDock Vina home page on http://vina.scripps.edu.
AutoDock Vina 1.1.1 (Apr 20, 2010) November 2010 AUTODOCK(1)