hi Justin thank you for your kind update:),
Towards the 1. Deuterium Order Parameters membrane analysis, I think the DPPC from the CHARMM-GUI generation´s numbering is different which it seemed to be upon inspection of its final coordinate file (also I have a heptamer) i.e. accordingly I received the below errors throughout. I would probably need to renumber the entire DPPC file in this case which may just be too much towards an analysis. If it something else repairable please let me know, thanks:) Joel
(base) Joels-Air:gromacs joelsubach$ gmx make_ndx -f step7_10.tpr -o sn1.ndx
:-) GROMACS - gmx make_ndx, 2022.1 (-:
Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /Users/joelsubach/Desktop/PANX1_PROJECT/MEMBRANE_IMPLANT/charmm-gui-OPM/gromacs
Command line:
gmx make_ndx -f step7_10.tpr -o sn1.ndx
Reading structure file
Reading file step7_10.tpr, VERSION 2022.1 (single precision)
Reading file step7_10.tpr, VERSION 2022.1 (single precision)
Going to read 0 old index file(s)
Analysing residue names:
There are: 3031 Protein residues
There are: 80536 Other residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
0 System : 358829 atoms
1 Protein : 48664 atoms
2 Protein-H : 24129 atoms
3 C-alpha : 3031 atoms
4 Backbone : 9093 atoms
5 MainChain : 12117 atoms
6 MainChain+Cb : 15022 atoms
7 MainChain+H : 15015 atoms
8 SideChain : 33649 atoms
9 SideChain-H : 12012 atoms
10 Prot-Masses : 48664 atoms
11 non-Protein : 310165 atoms
12 Other : 310165 atoms
13 DPPC : 71110 atoms
14 POT : 242 atoms
15 CLA : 214 atoms
16 TIP3 : 238599 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
a C34
Found 547 atoms with name C34
17 C34 : 547 atoms
a c36
Found 547 atoms with name C36
18 C36 : 547 atoms
a C37
Found 547 atoms with name C37
19 C37 : 547 atoms
a C38
Found 547 atoms with name C38
20 C38 : 547 atoms
a C39
Found 547 atoms with name C39
21 C39 : 547 atoms
a C40
Found 0 atoms with name C40
Group is empty
a C41
Found 0 atoms with name C41
Group is empty
a C42
Found 0 atoms with name C42
Group is empty
a C43
Found 0 atoms with name C43
Group is empty
a C44
Found 0 atoms with name C44
Group is empty
a C45
Found 0 atoms with name C45
Group is empty
a C46
Found 0 atoms with name C46
Group is empty
a C47
Found 0 atoms with name C47
Group is empty
a C48
Found 0 atoms with name C48
Group is empty
a C49
Found 0 atoms with name C49
Group is empty
a C50
Found 0 atoms with name C50
Group is empty
del 0-21
Removed group 0 ‘System’
Removed group 1 ‘Protein’
Removed group 2 ‘Protein-H’
Removed group 3 ‘C-alpha’
Removed group 4 ‘Backbone’
Removed group 5 ‘MainChain’
Removed group 6 ‘MainChain+Cb’
Removed group 7 ‘MainChain+H’
Removed group 8 ‘SideChain’
Removed group 9 ‘SideChain-H’
Removed group 10 ‘Prot-Masses’
Removed group 11 ‘non-Protein’
Removed group 12 ‘Other’
Removed group 13 ‘DPPC’
Removed group 14 ‘POT’
Removed group 15 ‘CLA’
Removed group 16 ‘TIP3’
Removed group 17 ‘C34’
Removed group 18 ‘C36’
Removed group 19 ‘C37’
Removed group 20 ‘C38’
Removed group 21 ‘C39’
13
Group 13 does not exist
Group is empty
q