Dear all,
After I change 67.OD1 and 110.NZ into :67.OD1 and
:110.NZ, the script starts work. Without :, he script
does not work for even several hours. What is more,
althugh the Pttaj does not work with ":", it does not
give any error message!
Best regards.
Fenghui Fan
--- Carlos Simmerling <carlos.csb.sunysb.edu> wrote:
> is it possible that the long time is because your
> mdcrd file is so large?
>
> Fenghui Fan wrote:
>
> >Dear all,
> >
> >I have the following script to measure the distance
> of
> >the 67.OD1 and 110.NZ in a protein during MD.
> However
> >when I run using $AMBERHOME/exe/ptraj *.prmtop <
> >distance.in, it takes very long time and never ends
> >for almost 1 hour thus I doubt there is something
> >wrong. Will you please take a look and see what is
> >wrong?
> >
> >------------------------------
> >
> >trajin complex_md1.mdcrd
> >distance DIST 67.OD1 110.NZ out 926MD1_distance.out
> >strip :WAT
> >go
> >
> >------------------------------------
> >
> >I am looking forward to getting your reply.
> >
> >Best regards.
> >
> >Fenghui Fan
> >--- Fenghui Fan <fenghui_fan.yahoo.com> wrote:
> >
> >
> >
> >>Dear all,
> >>
> >>I have the following distance.in script to
> measrure
> >>the distance of 67.OD1 and 110.NZ during md1 (a
> >>restricted md) and md2 (productive md):
> >>
> >>---------------------------
> >>
> >>trajin complex_md1.mdcrd
> >>trajin complex_md2.mdcrd
> >>distance first out 926cAMP_cAMPCOMPLEX_SALT.dat
> >>67.OD1
> >>110.NZ time 0.2
> >>strip :WAT
> >>go
> >>
> >>
> >>----------------------------
> >>
> >>Will you please tell me whether its correct or
> what
> >>kind of change I should modify it?
> >>
> >>I am looking forward to getting your reply.
> >>
> >>Best regards.
> >>
> >>Fenghui Fan
> >>
> >>
> >>__________________________________________________
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> >>
> >>
> >>
>
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> >>
> >
> >
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Received on Sun Oct 01 2006 - 06:07:07 PDT
