[gmx-users] How to use ambconv package...
tomas.kubar at uochb.cas.cz
Thu Jun 17 23:35:35 CEST 2004
> note that the fourth line of numbers has seven digits in amber7/8
> files, but only six in the amber6 files which ambconv was (I think)
> written for.
Yes! Ambconv doesn't work with amber7/8 prmtop files.
> There is also a bug in ambconv.c -- (thanks to Anton Feenstra for
> pointing this out).
I use ambconv version dated January 10, 2003 and I can't find such a bug
there. I noticed that Filip uploaded ambconv to the gmx site in
November, 2002. I'll have a look if there's a difference between these
two versions. Tomorrow, now I have to catch the bus..
>>I put the script file (filename is a) like
>># common name for file generation
>>ambconv -v \
>> -at ala.atop \
>> -gt ala.top \
>> -rst ala.rst \
>> -gro ala.gro
>>Too few command line arguments!AMBCONV v1.0
>>AMBER .top : ala.atop
>>GROMACS .top : ala.top
>>AMBER .rst : ala.rst
>>GROMACS .gro : ala.gro
>>Error: AMBER TOP: too few parameters on second line: Success
>>Error: AMBER TOP: too few parameters on third line: Success
>>Error: AMBER TOP: too few parameters on fourth line: Success
My input looks like
ambconv -v \
-at $MOL.atop \
-gt $MOL.top \
-rst $MOL.rst \
-gro $MOL.gro \
-pdb $MOL.pdb \
-common $COMMON \
and it works. So you may be missing the last 3 parameters.
Furthermore, I would like to pint out that it may be necessary to delete
the second (blank) line in the .gro file produced. (A bug that shouldn't
be difficult to remove, but.. :-)
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