Are you using ptraj? The 'closestout' keyword is only implemented in cpptraj.
-Dan
On Apr 12, 2012, at 5:30 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com> wrote:
> Hi all,
>
> I am using ambertools1.5 and encountered a problem when using the closest
> command. The script I am using is as follows:
>
> trajin traj.mdcrd 1 5 1
> trajout test.mdcrd nobox
> solvent byname WAT
> center :1-10 mass origin
> closest 20 :1-10 first closestout closestout.dat
>
> With this I can obtain the trajectory output test.mdcrd where the 20
> closest waters to residue 1-10 are selected. But no *closestout.dat* file
> was produced.
> In the manual it says that " If “closestout” is specified information on
> the closest solvent molecules will be print to
> <filename> with format:
> Frame Molecule Distance FirstAtom# "
>
> Could anybody please give me some hint on what might be wrong here please?
> Thanks!
>
> And if the closestout.dat is produced, what exact content is in this file
> please? Will the RESID or AtomID of the closest solvent be given as
> FirstAtom# please?
>
> Qiong
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Received on Thu Apr 12 2012 - 16:30:03 PDT
