Re: [AMBER] PDB Modification

From: Osman, Roman <roman.osman.mssm.edu>
Date: Mon, 30 Mar 2020 16:08:00 +0000

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
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