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 - 12:49:53 CDT

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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