David A. Case wrote:
> On Thu, Mar 01, 2007, Gustavo Seabra wrote:
>
>
>> That option is listed on Amber 9 manual, but whenever I try to use it, i
>> get:
>>
>>
>>> sander -O -i mdin -o mdout -y reaction.crd
>>>
>> mdfil: Error unknown flag: -y
>>
>
> Please see http://amber.scripps.edu/doc9/errata.html (look at second line)
>
> I know Carlos has talked about getting this working correctly for Amber 10,
> but I believe that has not yet been done.
>
> ....dac
>
>
Thanks Dave. But I must be missing something here... even with '-x' it
doesn't quite work. If I try:
sander -O -x reaction.crd -p vac.top
I get one of those ugly errors that it can't open unit 9 (the inpcrd
file). If I then include an inpcrd file, like:
sander -O -c inpcrd -x reaction.crd -p vac.top
sander now dies with the message:
POST-PROCESSING OF TRAJECTORY ENERGIES
Error in trajectory file
error in trajene()
But the trajectory in reaction.crd is ok (I tried openeing in vmd). So
it seems to me that just using '-x' instead of '-y' as suggested in the
erratum is not enough, or I am really missing something here...
Thanks,
Gustavo.
Received on Sun Mar 04 2007 - 06:07:46 PST
