are you sure that AMBER is installed correctly?
pleas chek ambpdb in bin directory
AMBERHOME/bin
On Sun, Jan 29, 2012 at 2:31 PM, leila karami <karami.leila1.gmail.com>wrote:
> Dear amber users
>
> I use amber for my system (protein).
>
> I did following steps similar to tutorial.
>
>
> 1) $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
>
> 2) protein = loadpdb "protein.pdb"
>
> 3) addions protein Na+ 0
>
> 4) solvatebox protein TIP3PBOX 8.0 iso
>
> 5) saveamberparm protein protein.prmtop protein.inpcrd
>
> there is no error in step 1-5.
>
> 6) $AMBERHOME/exe/ambpdb -p protein.prmtop < protein.inpcrd >
> final_protein.pdb
>
> but in step 6
>
> ERROR: syntax error.
>
> what is reason of this error?
>
> how to fix it?
>
> Best regards.
>
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Received on Sun Jan 29 2012 - 09:00:02 PST
