I would start by adding a best fit to the script. If it rotates and
translates you won't have a useful average. Even there there might be
distortions if the conformation changes. An average structure is not always
useful. I find that cluster analysis can be better for finding
representative structure(s).
On Sun, Jan 23, 2022, 9:03 AM A R <dhna_2001.hotmail.com> wrote:
> Dear Colleagues
>
> Hope all are well.
>
> I got distorted pdb structure from 10ns trj file within Amber18.
> These are two scripts used in cpptraj command:
>
> First script:
> "parm ../../../002.tleap/com.wat.leap.prm7
> trajin ../../33md.trj 1 200
> trajin ../../34md.trj 1 200
> trajin ../../35md.trj 1 200
> trajin ../../36md.trj 1 200
> trajin ../../37md.trj 1 200
> trajin ../../38md.trj 1 200
> trajin ../../39md.trj 1 200
> trajin ../../40md.trj 1 200
> trajin ../../41md.trj 1 200
> trajin ../../42md.trj 1 200
> strip :WAT,Na+
> center :1-43
> image familiar
> trajout 33_42reimaged.trj
> go"
>
> Second script:
>
> "parm ../../../002.tleap/com.wat.leap.prm7
> trajin ./33_42reimaged.trj
> average 33_42averaged_reimaged.pdb pdb nowrap"
>
>
> Could you please help solving the errors.
>
>
> Best regards
>
> Sincerely yours'
>
> Professor, Ph.D, (Full) Dr. Awwad A. Radwan
> (Current address: Pharmaceutical Technology center, Fac of Pharmacy, King
> Saud University, Al Ryiadh, Kingdom of Saudi Arabia, Office :
> +966-046-70562 Mob. 0505193925)
>
> (Home country address: Dept of Org Pharm Chemistry, Faculty of Pharmacy,
> Assiut University, Assiut, Egypt. Home Tel +2088-292164 Office Tel
> +2088-411326 Fax +2088-332776 Mobile 0103-716131)
>
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>
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Received on Sun Jan 23 2022 - 06:30:03 PST
