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owenvickery / cg2at

Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)
GNU General Public License v3.0
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Issues with CG2AT Backmapping - Peptidic bonds in cis configuration #26

Open GilbertoPPereira opened 1 year ago

GilbertoPPereira commented 1 year ago

Hello!

I was trying to backmap a system containing a protein embedded in a POPC membrane.

After running my system through CG2AT using the charmm36-jul2021 atomistic forcefield and martini_3-0_charmm36_Jul2021 as a fragment library, the rest as default, I went to VMD to check the structure and noticed that we had 84 peptidic bonds in cis configuration.

Could you please take a look? A folder containing the input CG structure and itps is attached to this email.

Best, Gilberto Pereira

CG2AT_CisPeptides.zip

LHRK commented 1 year ago

Hi!

I have come across the same issue in my protein system as well, backmapping to CHARMM ff. Has this been look at or what is the status?

pstansfeld commented 1 year ago

Thanks for flagging. I am taking a look at this.

LHRK commented 10 months ago

Hi! Has this been solved or what is the status?