During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list :
Group 0 ( System) has 180960 elements
Group 1 ( Protein) has 12511 elements
Group 2 ( Protein-H) has 6408 elements
Group 3 ( C-alpha) has 791 elements
Group 4 ( Backbone) has 2373 elements
Group 5 ( MainChain) has 3166 elements
Group 6 ( MainChain+Cb) has 3910 elements
Group 7 ( MainChain+H) has 3924 elements
Group 8 ( SideChain) has 8587 elements
Group 9 ( SideChain-H) has 3242 elements
Group 10 ( Prot-Masses) has 12511 elements
Group 11 ( non-Protein) has 168449 elements
Group 12 ( Ion) has 26 elements
Group 13 ( ZN) has 1 elements
Group 14 ( CL) has 1 elements
Group 15 ( NA) has 24 elements
Group 16 ( Water) has 168423 elements
Group 17 ( SOL) has 168423 elements
Group 18 ( non-Water) has 12537 elements
Group 19 ( Water_and_ions) has 168449 elements
There is no mention of Chains A and B. I would like to calculate H-bond between Chain A and Chain B and later do a SMD simulation between these two groups. However, I do not see them in the list.
How to fix this issue ?
Hi Agnivo! If you want to access particular molecules/groups you need to make an index file. Such options you can find by running make_ndx routine through a converted pdb-frame of your trajectory. In pdb-format different chains of proteins can be clearly seen. Gro-files won't show you that.
Dear Agnivo Gosai
When you consider itp files of chain A and chain B the number of atoms and residues of each chain is clear then you could specify each chain with make_ndx command.
Hope it helps
I tried doing make_ndx -f em.gro -n index.ndx
> "chain A | chain E"
it shows empty group
should i calculate the res id of each chain and try doing by that method ?
I have attached the PDB file.
This is the definition in the topol.top file :
[ molecules ];
Compound #mols
Protein_chain_A 1
Protein_chain_E 1
Ion_chain_A2 1
SOL 56141
NA 24
But when I do make_ndx - f em.gro -o index.ndx
> "chain A | chain E"
It shows empty group.
pdb file attached.
OK, let's assume that the list you pasted on your question is the list of the available groups when you type the make_ndx command.
You can see for yourself that you don't have any groups (with elements) named chain A or chain E.
In this case all you have to do is to create new groups with the elements that you want to include.
For example chain A is a group with aminoacids numbered from 1 - 32.
Hope this helps
Sotiris Papadatos
After using pdb2gmx on the cleaned PDB (only removed crystallographic waters), chain A has “resnr” from 19-615 and chain B has “resnr” from 333-526.
When I used make_ndx, how will it differentiate , as the numbers 333-526 are included in the IDs for the first chain as well. The total number of atoms for group protein does not equal to the two groups when I use make_ndx to create two separate groups by using “resnr”
As in the question group Protein has 12511 elements
This is what I observe upon using make_ndx :
> r 19-615
Found 12511 atoms with res.nr. in range 19-615
15 r_19-615 : 12511 atoms
> r 333-526
Found 6116 atoms with res.nr. in range 333-526
16 r_333-526 : 6116 atoms
I have attached the topology and gro file to explain my issue. Please have a look.
I see now. A minor suggestion then. Why don't you try using "gmx editconf -f processed.gro -o .gro -resnr 1". This will create a "unique" ascending number for all your residues (and ions, waters if any). Unless there is a specific reason that makes you keep the original residue numbers.
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