Hi,

it means that, on those particular lines of your topology, information for the dihedrals are missing.

You must add them to get rid of the errors.

Ricardo J Ferreira Thank you Sir. I will try to add the dihedral angle information in the topology.

Ricardo J Ferreira Sir, can you please tell me how to add such missing infomation - say a steps to add those missing dihedral angle information in topology.

thank you in advance.

Dear Shefin Basheera

Are you following Dr. Lemkul's tutorial on protein-ligand complex? In that case I would start over. The error means that something is missing in your forcefield (the dihedral types for the ligand in this case), which means that you made some mistake when you generated the ligand topology and added it to the main topology of your system. Try to go back and redo the passages.

P.S. If you are following that tutorial, and you got stuck at 'Adding ions' section, note that the tutorial expects a net charge of +6 (which is counterbalanced by 6 Cl- atoms in this step) while you have a -19, which probably points at some other problem in your ligand or (most likely) protein!

Hope this helps,

Nicola

Nicola Piasentin, it may not have been an error. The latest versions of Gromacs (2021 >) do not add some dihedrals, usually the amide bonds.

@Nicola Piasentin. Thank you for kind response. Yes, I followed Dr. Lemkul's tutorial. I will try it once again..

Ricardo J Ferreira good point. Shefin is using the 2018.1 version I think and the tutorial should be self-consistent (never did the ligand-one though)?

Anyway Shefin Basheera you have the stream file (http://www.mdtutorials.com/gmx/complex/Files/jz4.str) given by Justin and can convert this one with the python script from CGenFF website. Also it's better for you to use the same FF directory for the parameters in the script (charmm36-mar2019.ff) as the one used in the tutorial so you are sure to follow the same steps and can more easily double check for errors.

Nicola Piasentin Is updating gromacs to 2021 fine and will it help to overcome these kind of errors?

Thank you

Shefin Basheera

No, not at all. If anything, in general it is better to stick to the same exact steps as in the tutorial so that in principle you know where the error is in the moment you get a different output and/or an error in a step. This is true only if the tutorial is well made, which is absolutely true for those in that website.

The feeling is that you missed or did something wrong at the ligand topology stage, e.g. when you generated it or included it in the general topology of the system.