AMBER Archive (2009)

Subject: Re: [AMBER] create new crd files from transformed coordinates

• Previous message: wfli_at_biophy.nju.edu.cn: "[AMBER] question about pair wise per-residue energy decomposition; idecomp=3"
• In reply to: Donald Keidel: "[AMBER] create new crd files from transformed coordinates"
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On Tue, Mar 24, 2009, Donald Keidel wrote:

> I have ran minimization using amber and have generated coordinates using
> the -pqr option which creates a file that looks or is a pqr.
>
> I then apply a transformation (rotation and translation) to these
> coordinates and save them as another pqr. I then take the x,y, and z
> coordinates and make a file that has the same format as the original
> .crd file and run this new .crd file with the original .top file.
>
> I am getting a serious error and I think amber is not happy with the new
> .crd file. When I look at the 2 .crd files (original and new) I do not
> see a difference. I ahve the same spacing and significant figures and
> the order of the atoms is the same. Do I need to create a new .top file
> that corresponds to each .crd file? I thought the .top could be used
> with a transformed .crd as long as the atom order is the same.

What you did sounds correct, in principle. What is the "serious error" you
are getting? What makes you suspect the new .crd file? Have you tried
something really simple (like a single point minimization) with the new crd
file?

...dac

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• Previous message: wfli_at_biophy.nju.edu.cn: "[AMBER] question about pair wise per-residue energy decomposition; idecomp=3"
• In reply to: Donald Keidel: "[AMBER] create new crd files from transformed coordinates"
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