search

owenvickery / cg2at

Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)
GNU General Public License v3.0
29 stars 10 forks source link

Issue finding information for residue: CYSD #25

Open skaswur opened 1 year ago

skaswur commented 1 year ago

Dear users and developers,

Im running a simple test using a pure POPC membrane (boxsize10x10x10) generated by insane.py including PW and without protein. I run the following command cg2at -c bilayer.gro -w tip3p -o all -vv and continously get the following error:

"Issue finding information for residue: CYSD"

Is this due to a mismatch between the provided forcefield and provided fragments I am using? for Forcefield I would like to use charmm36 and opt for any of the charmm36 options when asked for it. For the fragments I have chosen (and combined others) mqartini_2 and 3 fragments. Nonetheless I keep getting the same issue. Some combinations yield the same issue but then for residue DAX.

Any mistake I am overseeing here? Can someone point me in the right direction?

andreashlarsen commented 1 year ago

HI. I cannot solve the issue, but I think the problem is that cg2at is looking for the amino acid CYSD (deprotonated cysteine, I think), which is not in the database/forcefields/charmm36-jul2022.ff/aminoacids.rtp file. If you don't have any CYS amino acids in your protein, it might be ok to make a dummy entry in aminoacids.rtp (e.g. copy CYS and rename this new residue as CYSD). It is not a proper solution to the issue, but may be a work-around to get things running... at least for a pure POPC membrane, I don't think this workaround would be problematic...

pstansfeld commented 1 year ago

I will fix.