Previous Thread
Next Thread
Print Thread
Really simple questions.
#1444 05/20/04 05:47 AM
Joined: May 2004
Posts: 222
C
chuan Offline OP
Forum Member
OP Offline
Forum Member
C
Joined: May 2004
Posts: 222
I have just been exposed to CHARMM a few days ago. And as my supervisor pointed out, intially learning it is a very steep up-hill slope.

I am hoping that i can ask questions but felt that they might be too trivial compared to the questions posed here. People might get bored and so on. Nevertheless i 'll try.

For example:

In a particular input file *.inp used to generate protein x, the following part reads:

open unit 1 card read name top_all22_prot.inp
read RTF card unit 1
close unit 1

open unit 1 card read name par_all22_prot.inp
read PARA card unit 1
close unit 1

is the ‘unit 1’ arbitrary?
What is the purpose for its existence?


CHARMM 30b1 driven by 1/ Xeon (32 bits) 2/ Redhat 7.3 (32 bits) with a Quadrics-modified 2.4-18-5 kernel 3/ Chuan, with 95% of the mentorship coming from great scientists frequenting this forum. 4/ Gracious support from the forum.
Re: Really simple questions.
chuan #1445 05/20/04 09:52 AM
Joined: Sep 2003
Posts: 4,783
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,783
Likes: 2
The unit used in CHARMM I/O is the Fortran unit; it is a simply speaking a number ("handle") that is used to indicate which file an I/O operation should be performed on.
For most things in CHARMM you don't have to us an explicit unit number (see most examples in Script Archive). In the cases when you need it you can use any number from 1 to 99 (upper limit is OS/compiler dependent), EXCEPT 5 and 6.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Really simple questions.
lennart #1446 05/20/04 08:20 PM
Joined: Sep 2003
Posts: 8,479
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,479
I have to disagree about the use of unit numbers; while the syntax has been relaxed for the simple case of opening and reading some standard CHARMM file types such as RTF, PARAM, PSF and COOR, there are many places where the unit numbers are still required:

  • file usage for the DYNAmics command; IUNREA, IUNWRI, IUNCRD, KUNIT, etc.
  • any place where one or more trajectory files are processed:

    • TRAJ command in CORREL
    • TRAJ I/O setup commands
    • COOR DYNA, COOR HBOND, and similar commands
    • MERGE command
    • etc.

  • output diversion via OUTU
  • writing data to a file with WRITE TITLE



Rick Venable
computational chemist

Re: Really simple questions.
chuan #1447 05/24/04 06:11 AM
Joined: May 2004
Posts: 222
C
chuan Offline OP
Forum Member
OP Offline
Forum Member
C
Joined: May 2004
Posts: 222
I submitted a job using the following command line:
bsub -n 2 par_charmm_script

The content of par_charmm_script:
#!/bin/bash
cd /home/yeohc/exercise_md
rm -f myprocfile
for i in `echo $LSB_HOSTS`
do
HN=`echo $i|cut -f 1 -d .`
echo "1 $HN:/home/yeohc/exercise_md /usr/local/charmm/exec/gnu/charmm-m" >> myprocfile
done
chmod +x myprocfile
prun -f myprocfile < minimize.inp > minimize.out


I have the following error:
/home/yeohc/.lsbatch/1085378646.345656: ./par_charmm_script: /bin/bash

: bad interpreter: Permission denied

What's wrong?


CHARMM 30b1 driven by 1/ Xeon (32 bits) 2/ Redhat 7.3 (32 bits) with a Quadrics-modified 2.4-18-5 kernel 3/ Chuan, with 95% of the mentorship coming from great scientists frequenting this forum. 4/ Gracious support from the forum.
Re: Really simple questions.
chuan #1448 05/24/04 12:15 PM
Joined: Sep 2003
Posts: 4,783
Likes: 2
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 4,783
Likes: 2
this is not a CHARMM error; it seems to be a unix problem with /bin/bash


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.008s Queries: 24 (0.004s) Memory: 0.9230 MB (Peak: 1.0126 MB) Data Comp: Off Server Time: 2020-08-08 23:20:17 UTC
Valid HTML 5 and Valid CSS