In the SwissPDB Viewer, there is an option called “aa making clashes” under the “Select” menu. This command will highlight the amino acid residues that are making bad contacts with its neighbors. To visualize the clashes, choose “by selection” from the “Color” menu.
-tl Print length of trajectories specified with ’-y’ to STDOUT. -ms <mask> Print selected atom numbers to STDOUT. -mr <mask> Print selected residue numbers to STDOUT. –mask <mask> Print detailed atom selection to STDOUT. –resmask <mask> Print detailed residue selection to STDOUT.
Perform symmetry-corrected RMSD calculation. This is done by identifying potential symmetric atoms in each residue, performing an initial best-fit, then determining which configuration of symmetric atoms will give the lowest RMSD using atomic distance to reference atoms.
distance d1-2 :1 :2 out d1-2.dat # geom 选项以mask 的几何中心来测距，而不是默认的质心 # mass 表示使用 mask 原子的质心而不是几何中心
dihedral phi :1@C :2@N :2@CA :2@C out phipsi.dat dihedral psi :2@N :2@CA :2@C :3@N out phipsi.dat
angle angle1 :2@N :2@CA :2@C out out.dat
You may need to go through the files and manually adjust any sections where the angle has jumped from -180 to +180 so that it looks clean when plotted, I won’t go into details on how to do this here but suffice to say you can do it in xmgrace with some code like:
parm topology.parm7 loadcrd mdcrd.nc ## 要不要先 fit 一下呢?? crdaction mdcrd.nc rms first @CA
crdaction mdcrd.nc average avg.pdb @CA parm avg.pdb reference avg.pdb parm avg.pdb crdaction mdcrd.nc rms reference @CA # Calculate atomic fluctuations for @CA only crdaction mdcrd.nc atomicfluct out fluct.dat bfactor @CA ---- parm myparm.parm7 trajin mytrajectory.crd rms first average crdset MyAvg run rms ref MyAvg atomicfluct out fluct.agr
atomicfluct out back.agr @C,CA,N byres bfactor # backbone
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The following COORDS data set commands are available:
combinecrd Combine two or more COORDS sets. crdaction Run a single Action on a COORDS set. crdout Write a COORDS set to a file. createcrd (Action) Create a COORDS set during a Run. loadcrd Create or append to a COORDS set from a file. loadtraj Create special COORDS set where frames remain on disk. reference Load a single trajectory frame as a reference.
average test.pdb pdb average test.mol2 mol2 start 1 stop 100 :1-10
trajin Input.nc average crdset MyAvg @CA run rms ref MyAvg @CA out RmsToAvg.dat run
closest 10 :1-151 first closestout closestmols.dat outprefix closest
Calculate the energy for atoms in .
对每一帧，计算和之间的非键相互作用 Periodic topologies and trajectories are required (i.e., explicit solvent is necessary A separate electrostatic and van derWaals cutoff can be applied, the default is 12.0 Angstroms for both
[<mask>] Atoms to calculate radius of gyration for; default all atoms [nomax] Do not calculate maximum radius of gyration. [tensor] Calculate radius of gyration tensor, output format ’XX YY ZZ XY XZ YZ’.
radgyr :4-10&!(@H=) out RoG.dat mass nomax
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surf [<dataset name>] [<mask>] [out <filename>]
(all solute atoms if no mask specified) using the LCPO algorithm of Weiser et al.. In order for this to work, the topology needs to have bond information and atom type information.
[lower <lower cut>] Cutoff for the first water shell (default 3.4 Angstroms). [upper <upper cut>] Cutoff for the second water shell (default 5.0 Angstroms).
A … H - D （A和D一般都默认为 O N F 原子） cpptraj中氢键定义为 A(受体重原子) … H(供体氢原子) - D(供体重原子)之间的相互作用。当A-D之间距离小于某值（3A），且A-H-D角度大于某值（默认为135°）时，判定氢键存在。 CPPTRAJ will also track solute to solvent hydrogen bonds and solvent bridging interactions (i.e. two or more solute residues hydrogen bonded to a single solvent residue).
Contact maps (matrices) are generated for native and non-native contacts. If byresidue is specified, contact maps are summed over residues, and contacts between residues spaced <resoffset> residues apart in sequence are ignored. If byresidue specified, the values for each individual atom pair are summed over the residues they belong to (this means for byresidue values greater than 1.0 are possible).
[distance <cut>] Distance cutoff for determining native contacts in Angstroms (default 7.0 Ang).
[resoffset <n>] (byresidue only) Ignore contacts between residues spaced less than <n> residues apart in sequence.
trajin ../equil_1-10.mdcrd #orient all frames best fit to backbone of helix in NMR structure rms first mass :2-20@CA,C,N #-- put all the pdb frames in a subdirectory trajout PDBfit/trp.pdb pdb
Do the clustering
ls -1 . > ../clustfils #ls -1 means single column
Remove first line since kclust can only handle < 50000 structures. We will fit structures 2 to 50,000. We need to remember that we did this as it means our pdbs actually start counting from two. This means that the ID’s in the centroid files will be off by one. You will see what I mean later. Here is the clustfils file.