separate different molecules in PDB

Just copy and paste the lines that belong to the molecule of interest. You may use the fields with the residue name or the chain name for orientation.

After pasting, the atoms might not be numbered from 1. Use pdb_atom_renumber.py to renumber your atoms. (Hack the source to renumber residues.)

setting the protonation state of a topology

pdb2gmx performs an automatic selection of the protonation state. Alternative (web) tools are H++ and PROPKA.

reconstructing missing residues

If only single residues are missing, you can use the profix utility of the Jackal software suite.

continue a simulation

run mdrun -deffnm PREFIX -cpi PREFIX.cpt

If trajectories contain data that was written after the creation of the last check-point, these data will be overwritten.

find the number of frames in a trajectory

gmxcheck -f TRAJECTORY

remove center-of-mass motion and rotation from a trajectory

In VMD:

• Go to Extensions > Analysis > RMSD Trajectory Tool
• check "Backbone" in Selection Modifiers
• press ALIGN

To save these coordinates

• right click Molecule entry in VMD main window > Save Coordinates
• select File Type "ttr"
• name & save

Using GROMACS tools:

trjconv -fit rot+trans -s SYSTEM.tpr -f TRAJECTORY.xtc -o OUTPUT.xtc

remove molecules / atoms from a gro file

editconf -ndef -f ORIGINAL.gro -o SELECTED_STRUCTURE.gro

In the interactive selection dialog, select the stucture of interest.

randomize velocities

When a tpr (binary topology) is created with grompp, you supply initial conditions in a .gro file. Only if the .gro contains velocity data and you specify the option gen_vel=no, velocities are taken form the .gro file. Otherwise new velocities are sampled from the Maxwell distribution.

(.gro files contain velocity data in the last three columns.)

using position restraints

genrstr -f TOPOLOGY.pdb -o RESTRAINTS.itp Attention: check if atoms are numbered in the right way, otherwise atom number of itp file might clash with numbers in the .pdb or .gro file.

Insert an include instruction for the RESTRAINTS.itp file in the TOPOLOGY.top file. Go to the [ moleculetype ] section in the .top file and add the lines:

#ifdef POSRES_XXX
#include "RESTRAINTS.itp"
#endif

Restraints will be activated, when you specify define=-DPOSRES_XXX in the .mdp file.

mixing graphical representations in VMD

• type in a selection in Graphics > Representations > Selections e. g. "resid 1 to 12"
• click Create Rep
• select the new Rep from the drop-down menu and change the selection e.g. "resid 13 to 100"
• going back to the Draw style tab, select a drawing method for each of the two Reps, e. g. NewCartoon and Surf.

show many frames at once in VMD

In Graphics > Representations > Trajectory > Draw Multiple Frames type first:last:stride

making videos in VMD

• Set backround color to white: color Display Background white
• disable axes triad: axes location off
• select Extensions > Visualization > Movie Maker, change settings in Movie Settings > Trajectory

moving molecules in VMD

On the VMD command line:

# only move residues 1 to 12
atomselect top "resid 1 to 12"
> atomselect0
atomselect0 moveby {1 0 0} # e.g. e_x
[atomselect top "all"] savepdb "MOVED.pdb"

Alternative: use key '7' and move molecule with the mouse pointer. Then chose File > Save coordinates.

deleting atoms in VMD

Example: remove all hydrogens from a PDB.

mol load pdb "FILE.pdb"
atomselect top "not hydrogen"
> atomselect0
atomselect0 writepdb "FILE_NO_H.pdb"

extracting a part of a trajectory

trjconv -b FIRST_TIME_STEP -e LAST_TIME_STEP -f INPUT.xtc -o OUTPUT.xtc

working with PDBs that contain two chains

Chain names are not supported in .gro file format. So always keep a PDB for your current topology. A good choice is the PDB you obtain after setting the box dimensions for your system.

To remove periodicity of the trajectories, you need a few tricks. Assume, that you work with a small ligand and a larger binding partner (the protein). Further assume that you want to center the protein in the simulation box. In the original data, the ligand would usually diffuse around and interact with different mirror images of the protein. Now you can map back the position of the ligand such that said mirror image of the protein sits at the center of the box.

Create an index file for the protein using make_ndx:

make_ndx -f SYSTEM.pdb -o PROTEIN.ndx

select the protein chain by typing chain X where X is the chain single letter code. Type q to save and exit. Map back coordinates using trjconv and this index file:

trjconv -n PROTEIN.ndx -s SYSTEM.tpr -f TRAJECTORY.xtc -o OUTPUT.xtc -pbc mol -ur compact -center

You can remove rotation of the protein, such that all ligand motion is relative to the protein. Add options

-fit rot

to the trjconv invokation.

display simulation box in VMD

pbc box_draw

disable automatic backup for Gromacs tools

export GMX_MAXBACKUP=-1