molecule contains no frames

[zypshine]

Sorry to bother. I really need some help. I have met a problem when I ran ::ligninbuilder::minimizestructures Spruce namd2 "+p4" in VMD 1.9.4 with CentOS 7. It gave an error "molecule contains no frames". More information could be found in the following. Something is wrong but I could't find where. Could you kindly give me some suggestions? Really thanks.

Running information: Info) Using plugin psf for structure file Spruce/L.psf psfplugin) WARNING: no impropers defined in PSF file. psfplugin) no cross-terms defined in PSF file. Info) Analyzing structure ... Info) Atoms: 145 Info) Bonds: 151 Info) Angles: 253 Dihedrals: 343 Impropers: 0 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 6 Info) Waters: 0 Info) Segments: 1 Info) Fragments: 1 Protein: 0 Nucleic: 0 Info) Using plugin pdb for coordinates from file Spruce/L.pdb Info) Finished with coordinate file Spruce/L.pdb. psfplugin) Structure requires space-delimited NAMD PSF format psfplugin) Writing angles/dihedrals/impropers... Info) Opened coordinate file Spruce/L.psf for writing. Info) Finished with coordinate file Spruce/L.psf. Info) Opened coordinate file Spruce/L.pdb for writing. Info) Finished with coordinate file Spruce/L.pdb. Info) Analyzing Volume... Info) Grid size: 56x53x45 (2 MB) Info) Total voxels: 133560 Info) Min: 0.000000 Max: 21.165998 Range: 21.165998 Info) Computing volume gradient map for smooth shading Info) Added volume data, name=density newvol Info) Using plugin namdbin for coordinates from file Spruce/out.coor Info) Finished with coordinate file Spruce/out.coor. ERROR molecule contains no frames

[jvermaas]

Ahh! So, there is a behavior problem here. In VMD 1.9.3, creating a density object (which is the volume that is being talked about) would place that density object into the same molecule as whatever was used to create it. However, in VMD 1.9.4, creating a density object makes a new molecule. This molecule has no frames, which gets us into problems. Internally, we fixed this by changing the internals of VMD so VMD 1.9.4 doesn't do this anymore, and behaves like VMD 1.9.3 does. I've made a change this morning that I think fixes this, but I don't have a stock VMD 1.9.4 anymore to test this on. Let me know how it goes!

[zypshine]

Thank you for your timely and helpful response. I have ran the latest version with VMD1.9.4 and it seems that it works partially. Running infromation in the Terminal and TkConsole is listed in the final. It's a pity that the same hint "molecule contains no frames" apprears again. But there is something different: 1) in the terminal, the info starts with Spruce/L0.psf in the latest version not Spruce/L.psf in the previous version. But it seems the code writes Spruce/L.psf and Spruce/L.pdb not Spruce/L0.psf and Spruce/L0.pdb finally. In the previous info, it started with Spruce/L.psf and wrote Spruce/L.psf and Sprcuce/L.pdb. 2) in the TkConsole, a lot of figures occur which don't show in the previous version. The figures belong to four arrays and they are almost same except that there is one more figure at the end of the fourth array. I wish these information could help.

In the terminal: Info) Using plugin psf for structure file Spruce/L0.psf psfplugin) WARNING: no impropers defined in PSF file. psfplugin) no cross-terms defined in PSF file. Info) Analyzing structure ... Info) Atoms: 145 Info) Bonds: 151 Info) Angles: 253 Dihedrals: 343 Impropers: 0 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 6 Info) Waters: 0 Info) Segments: 1 Info) Fragments: 1 Protein: 0 Nucleic: 0 Info) Using plugin pdb for coordinates from file Spruce/L0.pdb Info) Finished with coordinate file Spruce/L0.pdb. psfplugin) Structure requires space-delimited NAMD PSF format psfplugin) Writing angles/dihedrals/impropers... Info) Opened coordinate file Spruce/L.psf for writing. Info) Finished with coordinate file Spruce/L.psf. Info) Opened coordinate file Spruce/L.pdb for writing. Info) Finished with coordinate file Spruce/L.pdb. Info) Analyzing Volume... Info) Grid size: 51x54x46 (1 MB) Info) Total voxels: 126684 Info) Min: 0.000000 Max: 21.304129 Range: 21.304129 Info) Computing volume gradient map for smooth shading Info) Added volume data, name=density newvol Info) Using plugin namdbin for coordinates from file Spruce/out.coor Info) Finished with coordinate file Spruce/out.coor. ERROR molecule contains no frames

In the TkConsole 0 8 14 26 30 48 60 76 100 106 114 134 142 152 160 166 178 198 222 240 252 260 268 274 280 294 306 316 322 424 438 444 456 466 476 498 508 522 528 560 602 612 628 640 664 670 680 686 698 716 722 730 736 740 748 758 766 776 784 790 798 806 814 828 844 856 870 876 882 890 908 918 924 940 952 970 990 998 1008 1016 1026 1036 1044 1052 1058 1086 1092 1098 1104 1134 1142 1150 1160 1166 1174 1184 1188 1198 1204 1212 1224 1225 1226 1227 1228 1229 1230 1242 1258 1272 1284 1306 1318 1336 1348 1366 1378 1390 1406 1678 1690 1702 1944 1964 1978 1998 2176 2192 2226 2240 2556 2584 3008 3016 3098 3116 3210 3248 3304 3488 3514 3532 3570 3608 3644 3670 3716 3728 3760 3772 3818 4060 4432 4744 4776 4794 4806 4858 4872 4890 4906 4934 4946 5444 5456 5488 5510 5526 5548 5576 5598 5858 5866 6310 6338 6564 6580 6658 6676 6702 6714 6726 6742 6758 6772 6784 6796 6840 6868 6880 6892 6904 7022 7042 7486 7498 7514 7530 7542 7962 7982 8012 8036 8052 8084 8308 8338 0 8 14 26 30 48 60 76 100 106 114 134 142 152 160 166 178 198 222 240 252 260 268 274 280 294 306 316 322 424 438 444 456 466 476 498 508 522 528 560 602 612 628 640 664 670 680 686 698 716 722 730 736 740 748 758 766 776 784 790 798 806 814 828 844 856 870 876 882 890 908 918 924 940 952 970 990 998 1008 1016 1026 1036 1044 1052 1058 1086 1092 1098 1104 1134 1142 1150 1160 1166 1174 1184 1188 1198 1204 1212 1224 1225 1226 1227 1228 1229 1230 1242 1258 1272 1284 1306 1318 1336 1348 1366 1378 1390 1406 1678 1690 1702 1944 1964 1978 1998 2176 2192 2226 2240 2556 2584 3008 3016 3098 3116 3210 3248 3304 3488 3514 3532 3570 3608 3644 3670 3716 3728 3760 3772 3818 4060 4432 4744 4776 4794 4806 4858 4872 4890 4906 4934 4946 5444 5456 5488 5510 5526 5548 5576 5598 5858 5866 6310 6338 6564 6580 6658 6676 6702 6714 6726 6742 6758 6772 6784 6796 6840 6868 6880 6892 6904 7022 7042 7486 7498 7514 7530 7542 7962 7982 8012 8036 8052 8084 8308 8338 0 8 14 26 30 48 60 76 100 106 114 134 142 152 160 166 178 198 222 240 252 260 268 274 280 294 306 316 322 424 438 444 456 466 476 498 508 522 528 560 602 612 628 640 664 670 680 686 698 716 722 730 736 740 748 758 766 776 784 790 798 806 814 828 844 856 870 876 882 890 908 918 924 940 952 970 990 998 1008 1016 1026 1036 1044 1052 1058 1086 1092 1098 1104 1134 1142 1150 1160 1166 1174 1184 1188 1198 1204 1212 1224 1225 1226 1227 1228 1229 1230 1242 1258 1272 1284 1306 1318 1336 1348 1366 1378 1390 1406 1678 1690 1702 1944 1964 1978 1998 2176 2192 2226 2240 2556 2584 3008 3016 3098 3116 3210 3248 3304 3488 3514 3532 3570 3608 3644 3670 3716 3728 3760 3772 3818 4060 4432 4744 4776 4794 4806 4858 4872 4890 4906 4934 4946 5444 5456 5488 5510 5526 5548 5576 5598 5858 5866 6310 6338 6564 6580 6658 6676 6702 6714 6726 6742 6758 6772 6784 6796 6840 6868 6880 6892 6904 7022 7042 7486 7498 7514 7530 7542 7962 7982 8012 8036 8052 8084 8308 8338 0 8 14 26 30 48 60 76 100 106 114 134 142 152 160 166 178 198 222 240 252 260 268 274 280 294 306 316 322 424 438 444 456 466 476 498 508 522 528 560 602 612 628 640 664 670 680 686 698 716 722 730 736 740 748 758 766 776 784 790 798 806 814 828 844 856 870 876 882 890 908 918 924 940 952 970 990 998 1008 1016 1026 1036 1044 1052 1058 1086 1092 1098 1104 1134 1142 1150 1160 1166 1174 1184 1188 1198 1204 1212 1224 1225 1226 1227 1228 1229 1230 1242 1258 1272 1284 1306 1318 1336 1348 1366 1378 1390 1406 1678 1690 1702 1944 1964 1978 1998 2176 2192 2226 2240 2556 2584 3008 3016 3098 3116 3210 3248 3304 3488 3514 3532 3570 3608 3644 3670 3716 3728 3760 3772 3818 4060 4432 4744 4776 4794 4806 4858 4872 4890 4906 4934 4946 5444 5456 5488 5510 5526 5548 5576 5598 5858 5866 6310 6338 6564 6580 6658 6676 6702 6714 6726 6742 6758 6772 6784 6796 6840 6868 6880 6892 6904 7022 7042 7486 7498 7514 7530 7542 7962 7982 8012 8036 8052 8084 8308 8338 8339 namd2 +p4 Spruce/minimize.namd molecule contains no frames

[jvermaas]

Could you try again? I've just made an update that I think works around this problem.

[zypshine]

I have tried the new one. It works smoothly with all three libraries. The problem has been fixed successfully, which is really a happy thing. Thank you for developing and maintaining such a useful tool.