>From the output you posted it seems you ran the dssp command twice,
resulting in two data sets (DSSP_00004 and DSSP_00012), of which only
the latter is populated. Are you sure you're looking at output from
the second command? It's always more helpful to see the exact input
you're giving to cpptraj, as well as the complete output.
-Dan
On Sun, Dec 31, 2017 at 10:05 AM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Jan 02 2018 - 10:30:02 PST
