AMBER Archive (2009)

Subject: Re: [AMBER] extract frames from a .mdcrd

Date: Tue Feb 10 2009 - 02:52:19 CST

I suppose that this is the problem with the visualization Carlos, I'm
using iwarp=1, but I need it (but thanks, at least now I know why this
I've taken a look to the manual, and now I have differents pdb for
differents frames.
Other thing,
after this MD with AMBER I need use the CPMD program for QMMM
calculations, and for this I need a topology and a coordinate file. Is
for this reason that I want obtain this .crd (or .inpcrd) file, but I
don't find any option with ptraj, and whit Sander I obtain .mdcrd
Any suggestion?

Quoting Carlos Simmerling <>:

> you can use vmd to load the entire trajectory directly, and scroll
> through the frames.
> just make sure to image the trajectory first, since it may be that you
> did not set iwrap=1
> and your water has diffused. there is plenty of information about this
> in the archives (including examples) - search for ptraj and image (or
> look in the ptraj manual)
> On Fri, Feb 6, 2009 at 5:48 AM, <> wrote:
>> Dear amber users,
>> I've made a MD job. The output file seems correct, but when I check the
>> final structure in the restart file with the VMD (.rst file + .top file)
>> there are something wrong (appears a hole in the solvatation cubic box).
>> For this reason I want extract different frames from the mdcrd file. What is
>> the best option for made this? Can I visualize the frames directly with
>> ptraj? or I create a crd file with ptraj, and then I visualize this file
>> with VMD?
>> A lot of thanks,
>> Josť Luis
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