I barely discover Gromacs and I have to use it to study trajectory results, so I wanted to know if it was possible from an xtc file to generate several xtc files, one for each chain of the molecule that we want to study, (in order to retrieve information and perform calculations) and if it is possible, how? I found several information for concatenation or even to cut a simulation of time N in several simulations of time n, but I do not find anything concerning a possible cut according to the chains of the molecule.
Pretty easy:
A) use make_ndx to create an index of your chains
gmx make_ndx -f structure.gro -n previous_index.ndx -o new_index.ndx
use
splitch 1
to break down your protein into chains
(I am assuming your protein is group 1, as it usually is, if it has a different number just put the correct one)
press enter to list the groups
take note of haw your chains are named
press "q" to save
B) Now use trjconv to output your "trr" or "xtc" trajectory into a trajectory of selected goups
gmx trjconv -f traj.xtc -s topol.tpr -n new_index.ndx -o chain1_traj.xtc
when you run the command you will be asked to select the group for output.
choose the chain you need to isolate.
Now "chain1_traj.xtc" has the trajectory of only that chain.
You may also use the option flags:
-b start_frame -e stop_frame -skip write_only_every_this_frames
to select a portion of your data instead of the whole run.
C) Repeat as needed
You can repeat the operation for chain2 and so on.
Best wishes
Rogelio
You can make an index file. If your PDB file (system.pdb) has two chains A and B, then
gmx make_ndx -f system.pdb -o index_chain.ndx
>chainA
>chainB
q
Index file for multiple chains can be created in the similar way.
Later, separate xtc files for chains A and B can be generated using the index file
gmx trjconv -f md.xtc -s md.tpr -n index_chain.ndx -o md_chainA.xtc
Select chA group
gmx trjconv -f md.xtc -s md.tpr -n index_chain.ndx -o md_chainB.xtc
Select chB group
In case needed, separate tpr files can also be generated
gmx convert-tpr -s md.tpr -n index_chain.ndx -o md_chainA.tpr
gmx convert-tpr -s md.tpr -n index_chain.ndx -o md_chainB.tpr
As Anand said, you can make an index file and extract the interested part using the command "gmx trjconv".
thank you for your responses clear and precise, it help me a lot, I had no problem to apply your instructions.
sorry for my question of novice, I'm a little embarrassed to ask this question , but the trjconv function can also be use to generated pdb chain file from the files xtc, gro(or tpr) or file.pdb? To resume my question, the same system to generated xtc chain file exist to generated pdb chain file with gromacs? I know that we can used the pdb format as a trajectory format, so, I thought about it: gmx trjconv -f md.xtc -s md.gro -n index_with_chain.ndx -o chain1_traj.pdb
but the calculation time is really long what seems suspicious and I have not the results at the moment
You should use xtc format or other trajectory format as output format instead of pdb. Since they are binary file, it is easier for gromacs to read and write them, that is, make this process much faster than using a pdb format.
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