AMBER Archive (2009)

Subject: Re: [AMBER] ptraj image

From: Daniel Roe (droe_at_nist.gov)
Date: Wed Dec 09 2009 - 10:21:18 CST

The imaging commands can be a bit mysterious, at least to me. If you
haven't solved your issue yet, these commands have worked for me (FYI
this is for a 60 base, 30 bp ds DNA system), which is a slight variation
on what you have tried - I image one strand, then the whole duplex:

center :1-30 origin mass
image center origin
center :1-60 origin mass
image center origin

Also, first try your imaging commands independent of any other actions
that modify coordinates (such as an RMS calc) to see if that works
first. In my experience imaging and RMSD don't play well together.

Hope this helps!

-Dan

Taufik Al-Sarraj wrote:
> Hi Bill,
>
> do you mean
>
> {
> trajin cdsDNAc.mdcrd
> rms first mass out cdsDNAcimage.mdcrd
> go
> }
>
> I tried as many imaging commands as i could , the closest i got to do
> what i want is
> {
>
> trajin cdsDNAch1.mdcrd
> trajin cdsDNAch2.mdcrd
> trajin cdsDNAceq.mdcrd
> trajin cdsDNAcMD1.mdcrd
> trajin cdsDNAcMD2.mdcrd
> trajin cdsDNAcMD3.mdcrd
> trajin cdsDNAcMD4.mdcrd
> trajin cdsDNAcMD5.mdcrd
> trajout cdsDNAcc.mdcrd
> reference cdsDNAcmn2.rst
> strip :WAT*
> center :1-38 origin
> image origin center familiar
> rms reference mass out DNA.dat ':1-38' time 10
> rms reference out Naion.dat ':39-74' time 10
> go
> }
>
> using
> center :1-19 origin
> image origin center familiar
> center :1-38 origin
> image origin center familiar
>
> did not make much difference in my case.
>
> Thank you,
> Taufik
>
>
>>> the orientation of the dsDNA between the files changes making the movie
>>> unpleasant to watch. any suggestions?
>>>
>>>
>> Try an rms fit to 1st frame in the resulting trajectory.
>>
>> Bill
>>
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>>
>
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-- 
Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741

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