Hi, I have recently carried out Energy minimization of multichain protein and I have a few doubts about it. First GROMOS96 53A6 force field throws that there are too many errors, but I am almost convinced that it is harmless for simulation. I read that it is common issue and putting maxwarn in grompp commands will fix it, but I want to figure out if it is normal. Abstractly I have problem with resnr command. My npt.gro file has randomly numbered residues and I can’t select for example 1-60 residue because It is duplicated in all of my multichain residue list (I have five first residues etc.). Also I wonder how to define ngroups of my five-chain protein where two chains are one group and three other chains are secound group of my system. I have one pulling vector but at least 5 groups-chains of protein. I would appreciate a command sample to resolve this especially resnr command (I posted my attemption to renumber residues of this protein) and fragment of mdp file needed to define ngroups of pulling system). Thank you in advance.
I dont know understand what you wanted to ask. If you are looking for a way to define the pull groups, it is better to check your npt and manually define the index. Identify the residue/atoms and you can build with gmx make_ndx or create a index file and copy paste the atoms you need to specific group.
Thank You for answear but to do that I wonder how to renumber my npt.gro file. It has broken numeration and because of that I cant define my chain. Presumably I Need to have -renum flag in pdb2gmx command to fix it, but I dont know how to make this command correctly. The other problem is how to define pulling groups in pulling mdp file.
Also, the renumbering is not really important, you can still use the atom number of your system. So, for example, if the first two chains go from atom 1 to 10000 and the other three from 10001 to 50000, in gmx make_ndx you can do something like “a 1-10000” and “a 10001-50000” to define the two groups you need.
Lastly, but most importantly, you should never disregard errors, and you really have to have a strong and well argumented reason for using the -maxwarn flag. What errors are you muting?
