AMBER Archive (2006)

Subject: Re: AMBER: A script file for measuring the distance between 2 atoms during MD

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Sep 27 2006 - 14:44:08 CDT

Dear all,

After I change 67_at_OD1 and 110_at_NZ into :67_at_OD1 and
:110_at_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_at_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_at_OD1 and 110_at_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_at_OD1 110_at_NZ out 926MD1_distance.out
> >strip :WAT
> >go
> >
> >------------------------------------
> >
> >I am looking forward to getting your reply.
> >
> >Best regards.
> >
> >Fenghui Fan
> >--- Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:
> >
> >
> >
> >>Dear all,
> >>
> >>I have the following distance.in script to
> measrure
> >>the distance of 67_at_OD1 and 110_at_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_at_OD1
> >>110_at_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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