AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Sep 27 2006 - 12:59:33 CDT

does it give any output at all?

>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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