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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Received on Sun Jan 23 2022 - 06:30:02 PST
