here is the cpptraj out file
Warning: Not all BB atoms found for 2 residues: PRO:113 PRO:118
Info: This is expected for Proline and terminal/non-standard residues.
Info: Expected BB atom names: N=[N ] H=[H ] C=[C ] O=[O ]
CA=[CA ]
Info: Re-run with action debug level >= 1 to see which residues are missing
atoms.
Mask [:100-145] corresponds to 46 residues.
----- oxy_1.mdcrd (1-7000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 7000 frames and processed 7000 frames.
TIME: Avg. throughput= 63.6660 frames / second.
ACTION OUTPUT:
DATASETS (71 total):
RMSD_00001 "RMSD_00001" (double, rms), size is 7000
RMSD_00003 "RMSD_00003" (double, rms), size is 7000
DSSP_00004[None] "DSSP_00004[None]" (float), size is 0
DSSP_00004[Para] "DSSP_00004[Para]" (float), size is 0
DSSP_00004[Anti] "DSSP_00004[Anti]" (float), size is 0
DSSP_00004[3-10] "DSSP_00004[3-10]" (float), size is 0
DSSP_00004[Alpha] "DSSP_00004[Alpha]" (float), size is 0
DSSP_00004[Pi] "DSSP_00004[Pi]" (float), size is 0
DSSP_00004[Turn] "DSSP_00004[Turn]" (float), size is 0
DSSP_00004[Bend] "DSSP_00004[Bend]" (float), size is 0
DSSP_00012[None] "DSSP_00012[None]" (float), size is 7000
DSSP_00012[Para] "DSSP_00012[Para]" (float), size is 7000
DSSP_00012[Anti] "DSSP_00012[Anti]" (float), size is 7000
DSSP_00012[3-10] "DSSP_00012[3-10]" (float), size is 7000
DSSP_00012[Alpha] "DSSP_00012[Alpha]" (float), size is 7000
DSSP_00012[Pi] "DSSP_00012[Pi]" (float), size is 7000
DSSP_00012[Turn] "DSSP_00012[Turn]" (float), size is 7000
DSSP_00012[Bend] "DSSP_00012[Bend]" (float), size is 7000
DSSP_00012[res]:100 "ASN:100" (integer), size is 7000
DSSP_00012[res]:101 "LEU:101" (integer), size is 7000
DSSP_00012[res]:102 "ASP:102" (integer), size is 7000
DSSP_00012[res]:103 "ALA:103" (integer), size is 7000
DSSP_00012[res]:104 "LEU:104" (integer), size is 7000
DSSP_00012[res]:105 "HD1:105" (integer), size is 7000
DSSP_00012[res]:106 "ASP:106" (integer), size is 7000
DSSP_00012[res]:107 "HIP:107" (integer), size is 7000
DSSP_00012[res]:108 "LEU:108" (integer), size is 7000
DSSP_00012[res]:109 "ALA:109" (integer), size is 7000
DSSP_00012[res]:110 "THR:110" (integer), size is 7000
DSSP_00012[res]:111 "ILE:111" (integer), size is 7000
DSSP_00012[res]:112 "TYR:112" (integer), size is 7000
DSSP_00012[res]:113 "PRO:113" (integer), size is 7000
DSSP_00012[res]:114 "GLY:114" (integer), size is 7000
DSSP_00012[res]:115 "MET:115" (integer), size is 7000
DSSP_00012[res]:116 "ARG:116" (integer), size is 7000
DSSP_00012[res]:117 "ALA:117" (integer), size is 7000
DSSP_00012[res]:118 "PRO:118" (integer), size is 7000
DSSP_00012[res]:119 "SER:119" (integer), size is 7000
DSSP_00012[res]:120 "PHE:120" (integer), size is 7000
DSSP_00012[res]:121 "ARG:121" (integer), size is 7000
DSSP_00012[res]:122 "CYS:122" (integer), size is 7000
DSSP_00012[res]:123 "THR:123" (integer), size is 7000
DSSP_00012[res]:124 "ASP:124" (integer), size is 7000
DSSP_00012[res]:125 "ALA:125" (integer), size is 7000
DSSP_00012[res]:126 "GLU:126" (integer), size is 7000
DSSP_00012[res]:127 "LYS:127" (integer), size is 7000
DSSP_00012[res]:128 "GLY:128" (integer), size is 7000
DSSP_00012[res]:129 "LYS:129" (integer), size is 7000
DSSP_00012[res]:130 "GLY:130" (integer), size is 7000
DSSP_00012[res]:131 "LEU:131" (integer), size is 7000
DSSP_00012[res]:132 "ILE:132" (integer), size is 7000
DSSP_00012[res]:133 "LEU:133" (integer), size is 7000
DSSP_00012[res]:134 "HIE:134" (integer), size is 7000
DSSP_00012[res]:135 "TYR:135" (integer), size is 7000
DSSP_00012[res]:136 "TYR:136" (integer), size is 7000
DSSP_00012[res]:137 "SER:137" (integer), size is 7000
DSSP_00012[res]:138 "GLU:138" (integer), size is 7000
DSSP_00012[res]:139 "ARG:139" (integer), size is 7000
DSSP_00012[res]:140 "GLU:140" (integer), size is 7000
DSSP_00012[res]:141 "GLY:141" (integer), size is 7000
DSSP_00012[res]:142 "LEU:142" (integer), size is 7000
DSSP_00012[res]:143 "GLN:143" (integer), size is 7000
DSSP_00012[res]:144 "ASP:144" (integer), size is 7000
DSSP_00012[res]:145 "ILE:145" (integer), size is 7000
DSSP_00012[avgss]:1 "Para" (double), size is 46
DSSP_00012[avgss]:2 "Anti" (double), size is 46
DSSP_00012[avgss]:3 "3-10" (double), size is 46
DSSP_00012[avgss]:4 "Alpha" (double), size is 46
DSSP_00012[avgss]:5 "Pi" (double), size is 46
DSSP_00012[avgss]:6 "Turn" (double), size is 46
DSSP_00012[avgss]:7 "Bend" (double), size is 46
DATAFILES (2 total):
dssp.gnu (Gnuplot File): ASN:100 LEU:101 ASP:102 ALA:103 ... LEU:142
GLN:143 ASP:144 ILE:145
dssp.agr (Grace File): Para Anti 3-10 Alpha Pi Turn Bend
On Sun, Dec 31, 2017 at 7:27 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> Dear Amber users
>
> I have gnuplot of my system that is generated through cpptraj. this plot
> shows the black color mean not structure value assigned. while this
> residues region belong to turn or bend rather then none. kindly guide me
> how can i run the secstruct command without assigning the None from the
> script.
>
> Regards
>
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Received on Sun Dec 31 2017 - 07:30:02 PST
