You are here

C-term amidation

4 posts / 0 new
Last post
C-term amidation
#1

Hello,

I have been trying to use the Cterm_amidation patch, but everytime I use it in FastDesign or scoring it turns it back into a regular C terminus.

I've read the posts from other users, but I still can't make it work... What am I doing wrong?

Things I've tried so far:

I added "-include_patches Cterm_amidation" flag, both with the input file having a regular C terminus and with a neutral terminus - in this case I made sure the names of the atoms matched these in the patch:

ATOM    431  N   GLY A  27     -12.218  17.022  -3.254  1.00  0.00           N  
ATOM    432  CA  GLY A  27     -11.452  17.973  -4.051  1.00  0.00           C  
ATOM    433  C   GLY A  27     -11.747  19.407  -3.632  1.00  0.00           C  
ATOM    434  O   GLY A  27     -11.224  19.862  -2.675  1.00  0.00           O  
ATOM    435  H   GLY A  27     -12.840  17.370  -2.537  1.00  0.00           H  
ATOM    436  HA1 GLY A  27     -10.388  17.768  -3.938  1.00  0.00           H  
ATOM    437  HA2 GLY A  27     -11.694  17.841  -5.105  1.00  0.00           H  
ATOM    438  NT  GLY A  27     -12.495  20.191  -4.171  1.00 20.00           N  
ATOM    439  1HT GLY A  27     -13.037  19.899  -5.046  1.00 20.00           H  
ATOM    440  2HT GLY A  27     -12.613  21.177  -3.773  1.00 20.00           H  
TER     441      GLY A  27 

I also tried to use the flag -extra_patch_fa (path to the patch), or adding also -in:Ctermini C.

I'd be very grateful if anyone could find the error in what I'm doing!

Best regards

Anna

Category: 
Post Situation: 
Tue, 2021-03-02 07:46
tttt

Sorry to do a StackOverflow "marked as duplicate" but this topic has come up a few times and I think it may be quicker for you to hunt down past posts.
The last time I think is https://www.rosettacommons.org/node/11019

Wed, 2021-03-03 08:02
matteoferla

Hello,

Thank you for the reply, I read the post you linked and added ModifyVariantType to my script. I'm doing FastDesign, and I put the mover before it. The input structure has the terminus amidated already, and the atom names include NT.

However, first I get a message:

core.io.pose_from_sfr.PoseFromSFRBuilder: (8) [ WARNING ] can't find pose atom for file-residue 47 atom  NT  (trying to store temperature in PDBInfo)

Then:

ERROR: unable to find desired variant residue: ARG:CtermProteinFull ARG CTERM_AMIDATION

What may be the cause?

I hope this hasn't been asked before.

Thank you for the help!

 

Wed, 2021-03-03 09:22
tttt

 

Hi there,

I am facing a bit similar problem, I have TYR:Cterm_amidation in my peptide and I have checked the atom types and patch files as well but I still get following warnings:

core.util.switchresiduetypeset: [ WARNING ] When switching to centroid mode, a normal replacement type for residue TYR:CtermProteinFull:Cterm_amidation can't be found.
core.util.switchresiduetypeset: [ WARNING ]     an autogenerated replacement type is being used instead.
core.util.switchresiduetypeset: [ WARNING ] When switching to centroid mode, a normal replacement type for residue TYR:CtermProteinFull:Cterm_amidation can't be found.
core.util.switchresiduetypeset: [ WARNING ]     an autogenerated replacement type is being used instead.
 

core.chemical.Patch: [ WARNING ] Patch DimethylatedCtermProteinFull implies it can apply to residue type TYR:Cterm_amidation, but actually applying it fails.
core.chemical.Patch: [ WARNING ]    You may want to check your patch definitions.
core.chemical.Patch: [ WARNING ] Patch Cterm_amidation implies it can apply to residue type TYR:DimethylatedCtermProteinFull, but actually applying it fails.
core.chemical.Patch: [ WARNING ]    You may want to check your patch definitions.

 

There is also Cterm_amide group in the output pdbs. Should I ignore these warnings?

with kind regards

Mustafa

Fri, 2021-11-05 02:23
G Mustafa