I used to do it manually until my friend wrote a small routine to do it computationally.
Once you switch the C=O with the N-H the stereochemistry is inverted. The only thing to do is to renumber the residues, which is a pain when you do it manually. I should warn you that Pro is a problem, but a minimization takes care of it.
You can contact him directly: mihaly.mezei.mssm.edu<mailto:mihaly.mezei.mssm.edu>
Here is the site of the program called simulaid (it can do much more): http://inka.mssm.edu/~mezei/simulaid/
Good luck,
Rami
On Mar 30, 2020, at 11:55 AM, ankita mehta <mehtaroadies.gmail.com<mailto:mehtaroadies.gmail.com>> wrote:
You mean manually ..
I should interchange N to C and H to O manually in pdb file.
And for sequence inversion ?
I should rewrite the pdb file manually?
Ist copy the 15th residue and then 14th.....till 1.
Is not there any command to do it.
On Mon 30 Mar, 2020, 9:00 PM Osman, Roman, <roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>> wrote:
You can switch the C=O with the N-H.
The force field is the same so you can minimize it and that should do it.
Roman Osman
Sent from my iPhone
On Mar 30, 2020, at 9:45 AM, ankita mehta <mehtaroadies.gmail.com<mailto:mehtaroadies.gmail.com>>
wrote:
USE CAUTION: External Message.
Hii all,
I have a pdb file of say 15 residues.
I want to invert the sequence of residues i.e. i want (15,14,.........1)
from N terminal to C terminal.
without changing the coordinate positions.
Second i want to invert chirality also , all L- amino acid to D-amino
acid
conversion.
How this can be acccomplished ?
Thanks
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Roman Osman
Professor
Department of Pharmacological Sciences
Mount Sinai School of Medicine
New York, NY 10029
(212) 659-8627
roman.osman.mssm.edu<mailto:
roman.osman.mssm.edu>
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Received on Mon Mar 30 2020 - 09:30:03 PDT
