Subject: SUMMARY: problems running MOPAC from Sybyl ver. 6.1

From: [email-masked] (Jan Radomski)
Date: Mon, 7 Nov 1994 20:25:43 +0100

------
Dear All,

many thanks to all of you who replied to my plea for urgent help with
the problems running MOPAC from Sybyl ver. 6.1. 
As it turns out the reason is more complex than simple file permission
settings. Read mesage from Wayne Steinmetz below.

Have a good day,
Regards,
Jan P. Radomski

----------------------------
> Date: Sun, 6 Nov 1994 07:33:08 +0100
> From: janrad (Jan Radomski)
> Subject: problem running MOPAC from SYBYL 6.1
> ----
> Dear Netters,

> I have problem running MOPAC from SYBYL ver. 6.1,
> any attempt ends with some mysterious crashes.
> Any pointers would be greatly appreciated asap, 
> I must prepere class for students and there is no 
> support during weekends.

> Regards,
> Jan Radomski
===============================================================

Date: Sun, 6 Nov 1994 10:27:16 -0600
From: Mr. Berkley Shands <[email-masked]>
------
	See if your working directory is NFS mounted. You might have 
the classic "SYSVR4" security problem as follows...

server foo: exports disk /a. client machine xxx: mounts foo:/a on /b
(not an identical names path). You can use the /b device, but if you
cd /b; pwd; system V reams you with can't determine current directory.
Sometimes (on suns) you could fake the system out by aliasing "pwd" as 
"echo $cwd".
	Hope this helps...

	berkley Shands
================================================================ 

Date: Sun, 06 Nov 1994 11:30:51 -0700 (PDT)
From: Wayne Steinmetz <[email-masked]>
Subject: MOPAC with Sybyl
------
I just installed the R4000 version of Sybyl Version 6.1 and MOPAC on an Indy. 
Sybyl worked but MOPAC crashed.  The problem was solved with one call to
Tripos.  Here is what worked here.
1) You need swap space.  Tripos recommends 150 MB.  I reserved 200 MB.
The following UNIX commands were used.

mkdir -p /var/swap
/usr/sbin/mkfile 200m /var/swap/swap1
/sbin/swap -a /var/swap/swap1

To make the change permanent, add the following line to your /etc/fstab file.

/var/swap/swap1 swap swap pri=3

You can get a report on your current swap capacity by entering

/etc/swap -l

2) The V6.1 code for a R4000 processor has a bug!  You'll have to settle for
the R3000 code.  To install the code which works, insert your CD-ROM in the
drive and enter the following:

cd /$TA_ROOT
tar -xvf /CDROM/sybexe.tar bin/mopac

3) Make sure that NetBatch works and has been installed correctly.

I hope this works for your.

With best wishes,

Wayne Steinmetz
========================================================================

From: [email-masked] (Jonathan Baell)
Date: Mon, 07 Nov 94 13:23
-----
I have had a similar problem before.  It happened after I had run sybyl 
inadvertantly as root.  I subsequently tried to run some files in batch 
as a general user and wasn't allowed to because I didn't own the 
files....i.e. check the ownership of the user (I'm sure you have and you 
wouldn't think it a problem if rwx is OK, but it sounds like you want any 
help possible). 
+----------------------------------------------------------------------+
                  Dr Jonathan Baell
                  Senior Research Scientist
                  CSIRO,  Division of Animal Health                    
                  Private Bag 1, Parkville, Victoria 3052, Australia 
                  Internet email: [email-masked]               
                  Tel: +61 3 342-9782   Fax: +61 3 347-4042            
+______________________________________________________________________+

Date: Sun, 06 Nov 1994 09:57:43 EST
From: [email-masked]
-----
	Jan,
Check the underlying directory permissions of disk mount points.  We had
a similar problem when a mounted filesystem had good permissions but
the underlying mount point directory was only allowed restricted access.
To test this, simply dismount the filesystem and ls -l the directory
containing the mount point directory.

I hope this helps.

	Curt Breneman
	RPI Chemistry
===========================================================================

from: Jussi Eloranta <[email-masked]>
Subject: Re: CCL:problem running MOPAC from SYBYL 6.1
Date: Mon, 7 Nov 1994 09:11:15 +0200 (EET)
------
Have you checked the permissions on sybyl directories? (mopac interface
works on our system). Esp. check $TA_ROOT/bin, $TA_ROOT/bin/mopac* and
$TA_ROOT/batch/cmd or simply just do as root: chmod -R go+rx $TA_ROOT

Regards,
jussi
==========================================================================

From: Bob Funchess <[email-masked]>
Date: Mon, 7 Nov 1994 09:45:10 -0500
Organization: Molecular Simulations Inc.
Phone: (617) 229-9800 ext. 202
------
Dear Jan,
   We've had this problem reported from time to time.  It usually seems to
involve a directory somewhere in the path which doesn't have read
permissions (that is, while your current directory is 755, the parent
directory, or its parent, etc. might not be readable by you).  This
sometimes happens through some weird interactions with NFS, especially the
automounter.
    Regards,
           Bob Funchess
-- 
Dr. Robert B. Funchess                    [email-masked]
Senior Support Scientist                  Tel (617) 229-9800 x202
Molecular Simulations Inc.                FAX (617) 229-9899
16 New England Executive Park             http://www.msi.com/~bobf/bobf.html
Burlington, MA 01803-5297