Hi Rilei,
> When i tried to use antechamber, I found the errors as following:
> rileiyu.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
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /home/rileiyu/amber10/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 160; net charge: 0
>
> Running: /home/rileiyu/amber10/bin/mopac.sh
> 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 mopac.in 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
mopac.in. 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 mopac.in 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/mopac.sh from:
/server-home/netbin/amber10/bin/mopac >& FOR006
to
/server-home/netbin/amber10/bin/mopac > FOR006 2> FOR006
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 19 2009 - 23:00:03 PDT
