AMBER Archive (2004)

Subject: Re: AMBER: Re: Antechamber

From: Kara Wald (kdigiorgio_at_sbcglobal.net)
Date: Mon Nov 08 2004 - 15:49:13 CST

Ross,

Thanks for your previous advice. We applied the bugfixes and
recompiled Amber 8. When we attempted to run the test cases, it first
failed on Sander (?). This is what we got:

cd LES_GB; ./Run.LES
SANDER: LES+GB
  1: GB/LES w/o RDT test
STOP 0
diffing md.out.save with md.out
PASSED
==============================================================
  2: GB/LES with RDT test
STOP 0
diffing md_rdt.out.save with md_rdt.out
PASSED
==============================================================
cd qmmm/standard; ./Run.lysine

ҡRROR IN OPNFIL -- CANNOT OPEN UNIT 8 FILE |||#x8@H

  ERROR IN OPNFIL -- CANNOT OPEN UNIT 77 FILE B!

^[[?1;2c1525-001 The READ statement on the file fort.53 cannot be
completed because the end of the file was reached. The program will
stop.
   ./Run.lysine: Program error
make: *** [test.sander.QMMM] Error 1

We then ran the Antechamber test and it also failed. It gave us the
following:

[gibbs:local/amber/test] mccallum% sudo make test.antechamber
Password:
cd antechamber/tp; ./Run.tp
Running: /usr/local/amber/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /usr/local/amber/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 58; net charge: 0

Running: /usr/local/amber/exe/divcon

ҡRROR IN OPNFIL -- CANNOT OPEN UNIT 8 FILE |||#x8@H

Cannot open divcon.out , exit
   ./Run.tp: Program error
make: *** [test.antechamber] Error 1

We're working with Amber 8 that we got less than a month ago.

Thanks for all help,

Kara Di Giorgio
University of the Pacific
Stockton, CA

On Nov 4, 2004, at 1:31 PM, Ross Walker wrote:

> Dear Kara,
>
>> antechamber -i tp.pdb -fi pdb -o tp.mol2 -fo mol2 -c bcc
>>
>> I get the following:
>>
>> [gibbs:~] kwald% antechamber -i tp.pdb -fi pdb -o tp.mol2 -fo mol2 -c
>> bcc
>>
>> Total number of electrons: 58; net charge: 0
>>
>> Running: /usr/local/amber/exe/divcon
>>
>> ?ERROR IN OPNFIL -- CANNOT OPEN UNIT 8 FILE ??|||?#x8?@H
>>
>> Cannot open divcon.out , exit
>
> What version of Amber are you using? If it is version 8 then you
> should not
> need mopac since antechamber will use divcon for the QM calculations
> and
> this is shipped with Amber 8. Check that the path to divcon is
> correct. I.e.
> Is there a program called divcon in /usr/local/amber/exe/ ?
>
> Also check that amber is installed correctly. Can you run the test
> cases in
> $AMBERHOME/test? Do they all pass? Especially the antechamber ones.
>
> Also check that you have write permission in the directory that you are
> running antechamber. Unit 8 in divcon is the file named divcon.out so I
> suspect that the error is occuring when divcon is attempting to open
> the
> file divcon.out for writing. Does a divcon.out file currently exist in
> your
> directory? If so, do you have permission to edit / delete it? Can you
> create
> files in that directory? Are you over quota?
>
>> Does anyone know what is happening? How do I fix it? I read the
>> antechamber help page and found out that I needed to install
>> mopac and
>
> This is only for amber7 - amber8 does not require it.
>
> I would also advise applying all of the bugfixes
> (http://amber.scripps.edu/bugfixes.html) and recompiling amber and then
> trying it again. Especially make sure you run all the test cases.
>
> If you still have problems please get back to me.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>

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