Dear Prof.,
I have update the folder, please have a look, I am still trying to figure out the problem. The molecule is nucleotide in a triphosphate form and the nucleobase is a pyrrolo[2,1-f][1,2,4]triazin-4-amine.
Thank You
@SavioC even an energy minimization in vacuo fails and leads to a distorted molecule, so my only conclusion is that the topology you have generated for this molecule is of poor quality and should not be used.
Yes sir I noticed that too. Can you suggest any way to generate the topology. I am currently using PyRED to rectify.
My advice is to use CGenFF and follow my protocol in the protein-ligand tutorial, which it looks like you may have attempted at some point based on some of the files that were present. But whatever SwissParam gave you is completely broken somehow.
I am also having molecular distortion at many places right after
gmx pdb2gmx -f clean.pdb -o processed.gro -water spce (attached below)
but as soon as I reach to production(run01) part the structure seems fine.
attached below (after removing “SOL”)
gmx grompp -f production.mdp -c npt.gro -r npt.gro -c npt.cpt -p topol.top
No Broken part is seen.
You have a bad initial protein geometry that gets resolved after minimization and equilibration. Nothing terribly unusual here.
Thank you so much.
so its okay to go forward with the current structure selection and MD results will not be affected with this distortion happened at minimization level. right?
I don’t see a problem worth worrying about.
I didn’t look at your uploads, but depending on what you did and how poor the initial geometries were it’s possible for an EM to flip chiralities and/or introduce cis omega bonds. VMD has plugins that will test for those.