then the syntax is to use
-y <inptraj.
the prmtop file must match the inptraj - if you have stripped water or
anything else from teh traj file, you must make a matching prmtop.
you might also set ntwx=1 but I don't think that is needed.
does the test case pass?
On Sun, Nov 16, 2008 at 1:18 AM, Siddharth Rastogi
<siddharthrastogi08.gmail.com> wrote:
> yes i have attached all patches
>
> On 11/15/08, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>>
>> have you applied all patches?
>>
>>
>>
>> On Sat, Nov 15, 2008 at 10:33 AM, Siddharth Rastogi
>> <siddharthrastogi08.gmail.com> wrote:
>> > Dear Amber users,
>> >
>> > I am trying to calculate SASA using sander.
>> > Here is the input file
>> >
>> > SASA calculation
>> > &cntrl
>> > imin=5,
>> > gbsa=2,
>> > igb=1,
>> > ntb=0,
>> > surften=1,
>> > &end
>> >
>> > I have removed water from mdcrd file using ptraj.
>> >
>> > $AMBERHOME/exe/sander -O SASA.in -o SASA.out -p TY.top -c TY.crd -x
>> > TY.mdcrd
>> >
>> >
>> >
>> > if in the above line if I use -x TY.mdcrd :The error is : Unit 24 Error
>> > on
>> > OPEN: inptraj
>> >
>> > if I use -y TY.mdcrd : There is no error but under results I have the
>> > following :Post processing of trajectory energies and Trajectory file
>> > ended
>> > Can any one help me in this regard.
>> >
>> > Thanks in advance
>> >
>> > Siddharth Rastogi
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>
>
>
> --
> Siddharth Rastogi
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Received on Fri Dec 05 2008 - 14:56:18 PST
