It looks like maybe 2 lines at the beginning of the file? Fix that first
line and try again.
https://ambermd.org/FileFormats.php#trajectory
Bill
On 11/6/20 3:11 AM, Manisha wrote:
> Hello,
> I have been trying to find the Binding energy for protein DNA
> interaction. After preparing the .nc, .prmtop, and .mdcrd files for each of
> DNA, protein and complex, I gave the following command
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp
> tttgaa_complex.prmtop -rp tttgaa_prt_2.prmtop -lp tttgaa_2.prmtop -y *.mdcrd
>
> to which it shows the following error:
> Error: in read of Coords frame 1 of trajectory DNA.mdcrd.
> Error: Could not set up 'DNA.mdcrd' for reading.
> Error: Could not set up input trajectory 'DNA.mdcrd'.
> Error: Error(s) occurred during execution.
>
> I have stripped WAT AND IONS FROM EACH FILE. ALSO WHAT DOES IT MEAN BY
> "Could not set up 'DNA.mdcrd' for reading."
>
> I have attached my DNA.mdcrd file with the mail.
> please advise on how to and what to do
>
> Sincerely,
>
> *Manisha*
>
> *Ph.D. Scholar*
>
> Multidisciplinary Centre For Advanced Research and Studies
>
> Jamia Millia Islamia
>
> Delhi-110025
>
> Ph.no: 9518014737
>
>
> [image: Image result for save world by plant][image: Image result for save
> world by plant white background]
>
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Received on Fri Nov 06 2020 - 03:30:05 PST
