GROMACS version:2020
GROMACS modification: Yes/No
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Presumably you have a dimer, each chain of which is numbered from 1. The output RMSF graph numbers the residues exactly as they are in the topology, then XmGrace just does an odd thing where it tries to connect the different data sets, hence you get that odd line. If you have multiple chains, it is generally a good idea to analyze them separately so the data are in different files that can be plotted more conveniently.
gmx make_ndx -f step3_input.pdb -o index1.ndx The problem is that chain A Found 0 atoms with chain identifier A do you have any suggestion
Group is empty
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 696 Protein residues
There are: 85301 Other residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
0 System : 266871 atoms
1 Protein : 10998 atoms
2 Protein-H : 5506 atoms
3 C-alpha : 696 atoms
4 Backbone : 2088 atoms
5 MainChain : 2782 atoms
6 MainChain+Cb : 3434 atoms
7 MainChain+H : 3448 atoms
8 SideChain : 7550 atoms
9 SideChain-H : 2724 atoms
10 Prot-Masses : 10998 atoms
11 non-Protein : 255873 atoms
12 Other : 255873 atoms
13 UNK : 21 atoms
14 SOD : 24 atoms
15 TIP3 : 255828 atoms
nr : group ‘!’: not ‘name’ nr name ‘splitch’ nr Enter: list groups
‘a’: atom ‘&’: and ‘del’ nr ‘splitres’ nr ‘l’: list residues
‘t’: atom type ‘|’: or ‘keep’ nr ‘splitat’ nr ‘h’: help
‘r’: residue ‘res’ nr ‘chain’ char
“name”: group ‘case’: case sensitive ‘q’: save and quit
‘ri’: residue index
chain A
Found 0 atoms with chain identifier A
Group is empty
You can only select by chain identifier if they are actually present in the input PDB file. Presumably your file simply doesn’t have identifiers. Select by ranges of atom numbers if needed, or provide a file that has chain identifiers in it.
chain A consist of 1-348 residues but identified my pdp file so I created
r 1-348 & a CA
20 r_1-348_&CA : 694 atoms
0 System : 266871 atoms
1 Protein : 10998 atoms
2 Protein-H : 5506 atoms
3 C-alpha : 696 atoms
4 Backbone : 2088 atoms
5 MainChain : 2782 atoms
6 MainChain+Cb : 3434 atoms
7 MainChain+H : 3448 atoms
8 SideChain : 7550 atoms
9 SideChain-H : 2724 atoms
10 Prot-Masses : 10998 atoms
11 non-Protein : 255873 atoms
12 Other : 255873 atoms
13 UNK : 21 atoms
14 SOD : 24 atoms
15 TIP3 : 255828 atoms
16 chain : 12034 atoms
17 chain : 1044 atoms
18 A : 12034 atoms
19 ch : 12034 atoms
20 r_1-348&_CA : 694 atoms
gmx rmsf -s step5.tpr -f new.xtc -n index1.ndx -o CA1_rmsdf.xvg -res then
my graph is same error
If your two chains use the same residue numbers (which is the origin of the problem in the RMSF graph, as I noted above), creating a new index group using residue numbers will not yield any productive solution, since both chains will be selected. As I said, use atom numbers to create the groups.
