AMBER Archive (2009)

Subject: RE: [AMBER] Error: unable to find mopac charges in mopac.out

From: Rilei Yu (
Date: Tue Oct 20 2009 - 02:12:19 CDT

Dear Prof. Ross,

Thanks for your suggestion. When i did it as your suggestion, but the problem still cannot be solved.

1: I repeated to run it, but the same error appears again.
2: I have permission to delete these file, as I run it in my private computer.
3: I have attached all these files to this e-mail, can you re-check again?


Rilei Yu

--- 09年10月20日,周二, Ross Walker <> 写道:

发件人: Ross Walker <>
主题: RE: [AMBER] Error: unable to find mopac charges in mopac.out
收件人: "'AMBER Mailing List'" <>
日期: 2009年10月20日,周二,下午1:50

Hi Rilei,

> When i tried to use antechamber, I found the errors as following:
> rileiyu_at_imb09-02795:~/model/a9-a10-min/single$
> $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.mol2 -fo
> mol2 -c bcc -s 2
> Running: /home/rileiyu/amber10/bin/bondtype -j full -i
> Running: /home/rileiyu/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> Total number of electrons: 160; net charge: 0
> Running: /home/rileiyu/amber10/bin/
> ln: creating hard link `FOR005': File exists
> Error: unable to find mopac charges in mopac.out

This means that the file FOR005 already exists in your working directory.
When mopac is run the following script is used:

ln FOR005
/server-home/netbin/amber10/bin/mopac >& FOR006
mv FOR006 mopac.out
rm -f FOR0??

This creates a link for FOR005, standard in read by mopac, to the file In your case this file (FOR005) appears to already exist so the
link cannot be created. Mopac is then run using the existing FOR005 instead
of the link to and this probably runs with the wrong input, hence
the resulting error about missing charges. Note the last line of this script
removes all FOR0?? files which should include the FOR005 so you could just
try running it again and it may work the second time. If it does not then
check the ownership of the file FOR005 in your working directory. Perhaps it
is owned by somebody else and you do not have permission to remove it. Also
make sure you have permission to write to the directory you are running in.

On Ubuntu I have also found that you may want to change the following line
in $AMBERHOME/exe/ from:

/server-home/netbin/amber10/bin/mopac >& FOR006


/server-home/netbin/amber10/bin/mopac > FOR006 2> FOR006

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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  • application/octet-stream attachment: FOR005

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