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11

That is a modification of the standard XYZ file format and is called extended XYZ format, and not all programs are compatible with it. From the VMD Molfile Plugin Documentation page, it looks that VMD is only compatible with standard XYZ format. Also, take a look at this answer (to another question) about adding PBC info in VMD after loading standard XYZ ...


10

Don't Worry, it is not a problem, This happened because you used PBC (Periodic boundary condition) and VMD sometimes has bugs during the visualization in this case. The most important to you to see that the protein wasn't broken through all frames. You can solve this problem by using this command pbc unwrap -sel "protein" inside the Tk console as ...


9

Yes, It can. Just run this script in Extensions --> TK console of vmd before visualizing proc structure_trace {name index op} { vmd_calculate_structure $index } trace variable vmd_frame w structure_trace


8

To visualize the trajectory you can use VMD and use its pbctools vmd trajectory.xyz > pbc set {a b c alpha betta gamma} -all > pbc wrap where a, b, and c are the lattice vectors and alpha, beta, and gamma the angles. The angles can be omitted if the box is orthorhombic. For more information see here: https://www.ks.uiuc.edu/Research/vmd/plugins/...


8

In the VMD user guide different file formats natively handled by VMD are specified, including PSF and PARM that can both contain bond connectivity: PSF and PARM files contain atoms, residues, segment names, residue types, atomic mass and charge, and the bond connectivity. Depending on how your atoms and bonds are represented in python, you may choose to ...


8

You could use mol smoothrep x y z where x is the molid y is the representation number (starts from 0) z is the trajectory smoothining window size In your case, for molid 0 and for protein representation and trajectory smoothing window size of 5, the command will be mol smoothrep 0 0 5 and for representation of resname PEP, the command will be mol smoothrep ...


7

I usually use mol2 or psf formats to explicitly include bonds. mol2 works with many other programs (Avogadro, OpenBabel), while psf files are good for anything in CHARMM world (CHARMM, NAMD). The psf capabilities of VMD are good since it lives in CHARMM world as well.


7

First, You need to click on Create Rep and you will get a new line in the box below as the picture attached (with the same name "protein" in your case). To show the ligand, you should know the name of your ligand, to ensure about your ligand name, you can choose in the keyword "resname" and all the resname will appear in the value box. Or ...


6

Camps is correct, VMD cannot directly parse the comment line of an xyz file because the extended ASE format is not recognized. You can, however, use a tcl-script to load the file and parse the comment line yourself. I am no tcl expert but here is an example that works for me: set filename [lindex $argv 0] # load the coordinates into vmd mol new $...


6

I have found the solution to the problem. One needs to use the animate command to change the frame in the top molecule in VMD. The corrected script which produces the desired output is as follows: set outfile [open ./percent_helix.dat w] set lookup {H G I} set frame_num [molinfo top get numframes] set full [atomselect top "name CA"] set len [...


6

The problem in the sript I had written was that my system was not able to handle that many variables at one go. So I made the calculations piecewise i.e. 40 atoms at a time and the results closely match the values one gets from the inbuilt function. In any case, calculating RMSF for just the C alpha atoms gives more information about the structural changes ...


5

You have provided a LAMMPS data file as input to VMD and AFAIU, the default New Molecule option from VMD can't read this format. I am not sure how you are reading the given file, but I think the issue you are facing is due to the way you are reading the file in VMD. You can use the TopoTools plugin (which is available by default in VMD) to read this file. As ...


5

You can use ATOMSK. The command: atomsk initial.xyz -wrap final.xyz will wrap all the atom coordinates back into your simulation box. initial.xyz is your input file and final.xyz is the output after wrapping all atoms back into the simulation box. You can get the output in many different formats. ATOMSK is quite powerful and simple to use. Please have a look ...


4

One way could be as follow. Download software PACKMOL. Download the examples files (tar.gz or zip). Modify the file solvprotein-comment.inp: removing the info about the protein, and the ions and define the number of water molecules and the size of the droplet: # # Protein solvated by water and ions # # All atoms from diferent molecules will be at least 2....


4

Its neither a biophysical effect nor a bug in your MD simulation steps. It's just an visualisation issue. You could use the gmx trjconv command to make your protein and ligand to the center of the box and fit all atoms to a reference structure. gmx trjconv -s yourTpr.tpr -f yourTrr.trr -pbc mol -center -o yourTrr_centered.trr Clear details of individual ...


3

topo addbond x y should do the trick. where x is the index of the atom of an residue in which you are interested. if you want a more automated way, then you need to know the exact atom name and the residue number. Let's say, the residue number you are interested in is 250 and the atom name is HG1, and you want to add a bond to atom name OG1 of residue 267. ...


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