my current protein has SO4 as a cofactor, and it gives me this error when performing force field OPLS/AA
I tried removing SO4, but then protein seems to destabilize over time, any way to correct this??
Dear Vivek Js
1-"As in any simulation conducted with periodic boundary conditions, molecules may appear "broken" or may "jump" back and forth across the box "
you should center protein at simulation box and remove pbc condition for solve this problem: please use this command for do:
"
gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center -pbc mol -ur compact "
http://www.mdtutorials.com/gmx/complex/09_analysis.html
good luck
milad
I agree that the jumps in RMSD are nothing more than PBC effects.
Most SO4 found in PDB files comes from co-solvents or salts used for crystallization. Usually these are discarded for simulations in water because they are not biologically relevant.
In general, the solution to your error is found easily online:
http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database
this command is another option to extract trajectory without jumps: gmx trjconv -s md.tpr -f md.xtc -o md_nojump.xtc -pbc nojump
Note that using trjconv is not an "either/or" situation - you almost always need a few steps to properly re-image the trajectory. This is all spelled out on http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow
you must add so4 in aminoacid.rtp file of .ff
exactly such as other atom types
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