GROMACS version:2020
GROMACS modification: Yes/No
I applied md simulation my dna structure which is single-stranded by modelled for 100 ns .for rmsf analysis,I want to choose just residues which is only DC, DA,DT or DG.so I created make ndx using this command gmx make_ndx -f my input.pdb -o output.ndx but How to create these groups after this command I attached my screenshot.Could anybody help me please ?
Hi,
to create a group only with only cytidine residues you can use the option r
r DC
Does this answer your question?
\Alessandra
thank for your answer
may I ask one guestion ?
I created new groups just P atoms because for rmsd analysis I just want to select group P atoms in my single stranded dna system.for this reason,I wrote this command:
a P found 62 atoms with name P
then how to create and write my into output index file all P atoms ?
I am waiting for your respond Thank you so much
I think I have solved it Thank you