I tried the method, but my trajectory is 5000 frames long, and when I ran it, it gave me very huge energies. But when I do it frame by frame, the energies are normal looking.
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
On 30 Apr, 2014, at 9:43 pm, Brian Radak <radak004.umn.edu> wrote:
> This type of calculation is well-described on pages 285/286 of the Amber14
> manual
> and does not require any use of ptraj/cpptraj.
>
> Regards,
> Brian
>
>
> On Wed, Apr 30, 2014 at 9:28 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
>
>> Hi, I wish to ask about how the ptraj/cpptraj script would look like if I
>> were to extract each frame of a trajectory as individual .mdcrd files? I’m
>> doing this to calculate the protein’s energy frame by frame using imin=5.
>>
>> Thanks.
>>
>> Regards
>> Yip Yew Mun
>> Graduate, PhD
>> Chemistry and Biological Chemistry
>> School of Physical and Mathematical Sciences
>> Nanyang Technological University
>>
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>>
>
>
>
> --
> ================================ Current Address =======================
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> Institute for Quantitative Biology
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Received on Wed Apr 30 2014 - 09:00:03 PDT
