AMBER Archive (2004)

Subject: Re: AMBER: Ptraj data

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Tue Sep 21 2004 - 13:43:44 CDT

the 'time' option in 'rms' command should do this. You already specified
'time 0.5' in your input - this should dump 0.5,1.0,1.5,... in the first
column of your output - does this not work for you?
If I understood your description well (??), you're writing every 50ps,
so specifying 'time 50' (rather than time 0.5) might be what you want...

-Viktor

Steve Seibold wrote:
> Hello
> I have been using ptraj to get RMSd. However, when I get the data it
> places the number of frames (and not the time in picoseconds) on the
> x-axis. That is, I have 1000 frames with each at 2500 steps (50 ps).
> When I calculate the RMSd of a residue it gives me RMSd vs 1 through
> 1000 frames instead of time. The tutorial, using DNA, on the AMBER web
> page shows in their example that using ptraj gives the time in ps. I
> would like the RMSd for every ps or so and not for each frame where each
> frame consists of 50ps. Could someone help me?
>
> I am using AMBER7 and my input file is as follows:
>
>
> trajin HIV_N25D3.mdcrd
>
> trajout HIV_N25D3_1.mdcrd nobox
>
>
>
> box x 51.1333056 y 50.7934380 z 72.183431
>
> center :1-99 origin
>
> image :100-198 origin center familiar
>
> rms first out N25D3_data1 :1 time 0.5
>
> rms first out N25D3_data2 :2 time 0.5
>
> rms first out N25D3_data3 :3 time 0.5
>
> average N25D3_avg.pdb :1-99 pdb
>
> strip :WAT
>
> go
>
>
>
> Any ideas would be greatly appreciated.
>
> Thank you,
>
> Steve
>

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