## SPDB-Viewer 显示 clashes 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.
reference: Use the first loaded reference structure. refindex <#>: Use reference index number <#> (so 'reference' is like 'refindex 0'). ref <name | tag>: Use reference specified by file name or tag.
parmindex <#>: Use topology index number <#>. parm <name | tag>: Use topology specified by file name or tag.
rms ToMember1 :1-13&!@H= reference out rmsd2.agr rms ToMember10 :1-13&!@H= refindex 1 out rmsd2.agr rms ToLast :1-13&!@H= ref [last] out rmsd2.agr # out的文件名一样的话，会都输出到这个文件，不会覆盖，可以用xmgrace一起查看
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
COORDS 相关的操作
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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.
默认以第一个分子的质心为中心 [firstatom] 选项: Image based on molecule first atom; default is to image by molecule center of mass.
image
一般使用 autoimage 就足够了 For periodic systems only, image molecules/residues/atoms that are outside of the box back into the box.
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center :1 image
## unwrap 与image 相反??
重设 box center
Move all atoms so that the center of the atoms in is centered at the specified location: box center (default), coordinate origin, or reference coordinates
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
选定距离mask最近的水分子
closest 10 :1-151 first closestout closestmols.dat outprefix closest
energy
Calculate the energy for atoms in .
lie
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
计算溶剂可及面积(单位A^2)
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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.[122]. 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).
氢键分析
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.
[mindist] If specified, determine the minimum distance between any atoms in the mask(s). [maxdist] If specified, determine the maximum distance between any atoms in the mask(s).
[byresidue] Write out the contact map by residue instead of by atom.
按残基编号 :1-10 = "residues 1 to 10" :1,3,5 = "residues 1, 3, and 5" :1-3,5,7-9 = "residues 1 to 3 and residue 5 and residues 7 to 9"
按残基名称 :LYS = "all lysine residues" :ARG,ALA,GLY = "all arginine and alanine and glycine residues"
按原子编号 @12,17 = "atoms 12 and 17" @54-85 = "all atoms from 54 to 85" @12,54-85,90 = "atom 12 and all atoms from 54 to 85 and atom 90"
按原子名称 @CA = all atoms with the name CA (i.e., all C-alpha atoms) @CA,C,O,N,H = all atoms with names CA or C or O or N or H (i.e., the entire protein backbone)
按距离选择残基或者原子 [:5 <@4.5] all atoms within 4.5A from residue 5 [(:1-55 <:3.0) & :WAT] all water molecules within 3A from residues 1-55
[:1-10@CA] is equivalent to [:1-10 & @CA] [:LYS@H=] is equivalent to [:LYS & @H=]
:*&!@H= All non-hydrogen atoms (equivalent to "!@H="). @CA,C,O,N,H All backbone atoms. !@CA,C,O,N,H All non-backbone atoms (=sidechains for proteins only).
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
pdb重新编号(将 1,10,100变成001,010,100)
教程里有对应脚本，不如自己写一个
Do the clustering
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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.
awk -f extract_centroids.awk Centroid_6 | tee Centroid_6.stats
查看与聚类中心最接近的结构的编号
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sort -n -k2 centroid03.member.dat | head -5 # Sort the member file numerically on the second column (rms distance from the centroid).
cp PDBfit/trp.pdb.21341 centroid03_bestmember.pdb
Plot the RMS distances from the centroids
先将 centroid0*.member.dat 等导入到xmgrace
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In xmgrace you can then do (xmgr menus may differ slightly):
Bring up Set Appearance window from xmgrace Plot menu Select all sets set Line properties Type to None set Symbol properties to Type circle and adjust Size to 16 click Apply (at bottom)
Select each set, and change the Symbol colors (press Apply after selecting each color):