Hello Sir, please make video trail for Peptise Peptide MD simulations on Gromacs please, there is no a single video tutorial on youtube for Such MD Simulations . Thanks
Fatal error: Group CNT referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. In my topol.top file, the [moleculetype] names is CNT, why did this error happen? What is the index file? I have attached the npt.mdp file. Can anybody help me?
explanation of the contents of each mdp file is necessary. If we can't see or understand the mdp files,we can't modify the files. Explanation of mdp files is higly appreciable.
Fatal error: The residues in the chain MET1--NI602 do not have a consistent type. The first residue has type 'Protein', while residue KCX219 is of type 'Other'. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS does anyone know how to solve this?
I appreciate your efforts but this more are like technical presentation "click this , click that" . This would have been more interesting if you could have explain the subject behind each commands and arguments.
Would highly appreciate a tutorial for md simulation of protein-ligand complex.
On which basis select salt for solvation.For all complexes NaCl or other salt options.Any guide there.
Hello Sir,
please make video trail for Peptise Peptide MD simulations on Gromacs please,
there is no a single video tutorial on youtube for Such MD Simulations .
Thanks
How to continue the discontinued MD simulation?
hi sir, i am sorry. If we did triplicate md simulation. How to make an average graph of triplicate md simulation in xmgrace? Thank you Sir!
if you are keeping the same pH as its's isoelectring point ,then it will precipitate in experimental condition ?!!!
"Mn parameter is not in database" what to do???
how we get all 5 important file mdp.itp etc files
Fatal error:
Group CNT referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.
In my topol.top file, the [moleculetype] names is CNT, why did this error happen? What is the index file?
I have attached the npt.mdp file. Can anybody help me?
nabila ouassaf if you work on protein ligand simulation , the index file is important , this tutorial for only apo protein
Pls remove Hetro atom in ur PDB file
Good morning Sir. This is very nice tutorial. Could you please make a video on Replica Exchange MD in Gromacs from the scratch. Thank you
Thanks for sharing the information
Please share the tutorial file.
explanation of the contents of each mdp file is necessary. If we can't see or understand the mdp files,we can't modify the files. Explanation of mdp files is higly appreciable.
Thank you..Useful
Thank you
great job sir
Fatal error:
The residues in the chain MET1--NI602 do not have a consistent type. The first
residue has type 'Protein', while residue KCX219 is of type 'Other'. Either
there is a mistake in your chain, or it includes nonstandard residue names
that have not yet been added to the residuetypes.dat file in the GROMACS
does anyone know how to solve this?
I get the same error, did you manage to solve it?
@@SaurabhShukla_22 put " --missing" at the end of the command
Thanks
I appreciate your efforts but this more are like technical presentation "click this , click that" . This would have been more interesting if you could have explain the subject behind each commands and arguments.