VMD/NAMD rmsd_residue_over_time returns no atoms selected

2
votes

Whenever I run the rmsd_residue_over_time function from the residue_rmsd.tcl script from UI VMD/NAMD tutorial, it returns the error "no atoms selected". Specifically, I input the following, after loading my psf file and 20000 frames of my dcd file:

Main< (VMD) 80 % set sel_residue [atomselect top "protein and alpha"]
atomselect34
Main< (VMD) 81 % rmsd_residue_over_time top $sel_residue
Calculating rmsd for frame 0 ...
measure rmsd: no atoms selected

To check that I have atoms selected:

Main< (VMD) 82 % $sel_residue get index
4 21 35 46 56 72 89 106 128 147 157 167 186 201 223 234 245 252 259 283 302 309 325 335 354 373 385 399 409 421 435 449 466 485 504 525 549 556 568 583 607 629 641 658 669 680 694 705 727 743 760 770 780 790 800 816 835 857 874 885 900 914 931 953 970 989 1008 1022 1041 1053 1069 1084 1103 1127 1139 1149 1161 1180 1196 1210 1231 1247 1259 1278 1288 1303 1325 1342 1358 1372 1379 1393 1410 1424 1443 1453 1468 1487 1498 1508 1518 1528 1547 1564 1585 1596 1608 1622 1636 1646 1663 1677 1699 1718 1737 1747 1764 1783 1790 1799 1811 1818 1825 1841 1855 1865 1885 1895 1919 1929 1948 1955 1967 1982 1996 2016 2040 2059 2071 2095 2109 2124 2135 2149 2168 2182 2196 2206 2227 2239 2246 2260 2272 2296 2308 2322 2336 2352 2364 2388 2398 2415 2425 2442 2456 2475 2499 2516 2535 2549 2568 2575 2592 2602 2621 2628 2643 2657 2674 2698 2708 2725 2744 2760 2774 2798 2817 2839 2846 2860 2874 2888 2895 2905 2915 2926 2945 2969 2979 2986 3007 3019 3033 3044 3068 3082 3098 3105 3117 3139 3153 3160 3171 3181 3193 3214 3221 3235 3249 3263 3275 3294 3304 3320 3339 3365 3380 3397 3404 3428 3440 3452 3471 3487 3506 3522 3536 3557 3577 3591 3610 3622 3639 3656 3670 3680 3695 3706 3730 3754 3766 3782 3801 3811 3822 3832 3842 3866 3885 3904 3914 3929 3936

Has anyone else encountered this error before?

2
vmd

2 Answers

0
votes

I wasn't able to solve the issue per se, but by loading the PDB on top of the PSF (which the tutorial from the University of Illinois doesn't specify), I was able to get it to run properly.

0
votes

It's late but it could be useful for other people: the rmsd_residue_over_time function from the residue_rmsd.tcl script contains the following lines:

set ref [atomselect $mol "chain U and resid $r and noh" frame 0]
set comp [atomselect $mol "chain U and resid $r and noh" frame $frame]

And chances are there is no "chain U" in your structure. Just change the chain to the appropriate letter or remove the chain selector alltogether.