AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 10 2009 - 04:58:12 CST


use the trajout command of ptraj with "restart" option. check the manual for
the exact syntax. it will write inpcrd format.

On Tue, Feb 10, 2009 at 3:52 AM, <vallespardojl_at_chem.leidenuniv.nl> wrote:

> 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 problem).
> 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 <carlos.simmerling_at_gmail.com>:
>
> 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, <vallespardojl_at_chem.leidenuniv.nl>
>> 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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>>>
>>>
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>
>
>
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