When I load repeat simulation of my mutated protein from 10ns-20ns-30ns, its RMSD graph is in picture. I watched my dcd, my protein goes out of the water box. I tried to put it inside of the box with "pbc wrap -centersel "protein" -center com -compound residue -all" code. The protein entered the box but the RMSD values doesn't change. How can I solve this problem?
I asumed you use Gromacs package for rmsd calculation.
So first you should remove all pbc issue in your trajectory file. Try following steps:
1. If your system contains protein+ligand, make an Index file having group of protein+ligand
2. gmx trjconv -f xxx.xtc -s xxx.tpr -n index.ndx -o xxx_nowater.xtc -pbc cluster
select group number of protein+ligand.
3. now calculate rmsd using xxx_nowater.xtc with option of using -s npt.gro file (instead of using .tpr file).
Hope it will work
Try to remove all pbc and try to calculate RMSD. For nopbc file.
Try to create your xtc file with out pbc and calculate RMSD for this trajectory.
In this plot,the rmsd value showing high destabilized and fluctuated due to your protein stricture,please check with out ligand,and with ligand.
I am thinking this RMSD for protein-protein complex. if this is correct then you have to generate the separate index file for both chain and can generate the RMSD plot
Hi,
As everyone mentioned, pbc could be the main issue. You can follow the trjconv pipeline given in gromacs documentation. Here is the link, http://www.gromacs.org/Documentation_of_outdated_versions/Terminology/Periodic_Boundary_Conditions
Also, please make sure you choose same groups while RMSD calculation and you can choose npt.gro for your reference structure flag.
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