Remember, Tcl's generic syntactic parsing happens first, before command arguments are interpreted semantically. Without quoting, Tcl doesn't know that that's meant to be one word the generic parsing layer decides there's really four words there ( set, ag_around_water, resid and the complex ) and tells set to deal with that, which it doesn't like. It's usually best to avoid using them like that. Now, spaces are legal in variable names, but then the variable name needs to be quoted, and that can get a bit annoying. Has what appears to be a space instead of an underscore in the variable name. However, in this case we can look through and see that this line near the bottom of the script: set ag_around_water resid vmd> set protein atomselect top 'protein' Your email address will not be published psf file contains important information about the system such as which atoms are bonded together, what charge they are, and the mass of each atom type, but does not contain any spatial information vmd) and run the following from terminal: vmd -dispdev text -e FILENAME (i In Charmm and NAMD, the PSF file. But with the command in VMD,that is set dna > atomselect top dna and measure sasa 1.4 dna,the result is opposite > to arrise. If you examine the stack trace (usually printed with the error message when using standard tclsh, though it's changeable with user code) then you'll get told where the problem happened. Observe water molecules that close to LIG(lipid): all and within 5 of resname LIG. In this case, it's coming from the set command, and indicates that you've either said set on its own, or given more than two further arguments to it. Is a standard error thrown when a built-in command gets the wrong number of arguments to evaluate. RMSD/RMSF setup set start atomselect top 'protein and backbone' frame 0. If the residue numbers differ between the two structures, a cumbersome, though simple workaround is to specify the residue name, or some other attribute that is different between the 2 structures, in addition to the number, e.g.
![vmd atomselect vmd atomselect](https://i1.rgstatic.net/ii/profile.image/468273767686145-1488656574551_Q128/Gourav-Shrivastav.jpg)
Wrong # args: should be "set varName ?newValue?" To load the trajectory file into the VMD software, a new molecule must be. Now you can type a list in the atomselect box, e.g.
![vmd atomselect vmd atomselect](https://img2020.cnblogs.com/blog/1869699/202004/1869699-20200411102758419-729513731.png)
The newly created atom selection is a Tcl proc, which takes the following options. Puts $outfile "$pid $k] $ag_around_water_resname A: $water_around_b_resname" vmd> atomselect top within 5 of resname LYR frame 23 atomselect2. opens the file that has the atoms that are to be restrained if amber inputs do this mol load parm7 parm.file rst7 crd.file if namd inputs do this mol load psf. #count water molecules between chain A and chain C or between #chain B and chain C Lets 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. if you want a more automated way, then you need to know the exact atom name and the residue number. Note: The script includes terms specific to VMD program, such as mol and resid. where x is the index of the atom of an residue in which you are interested.
![vmd atomselect vmd atomselect](http://1.bp.blogspot.com/-xWE2SF_3Lcw/UgOmFAzXwBI/AAAAAAAAHkY/tiJY1zxciow/s1600/Screen+Shot+2013-08-08+at+10.02.37+AM.png)
I tried to run the following Tcl script and got the error: wrong # args: should be "set varName ?newValue?"