[AMBER] RDF analysis

From: Shaikh Abdul R S Ramaju <smasarsr.nus.edu.sg>
Date: Tue, 23 Feb 2010 16:05:58 +0800

Dear Amber Users,

 

I am using ptraj to calculate Radial distribution function. I would like
to analyze which part of the organic solvent molecule interacts with
protein residues (1-129).

I used the following command to calculate RDF

 

trajin MD3.crd

radial md3_hyd 0.05 40 :UNK.C4,C5,C6 :1-129 closest (default density of
water 0.033)

 

In another case I used density of solvent molecule

 

radial md3_hyd 0.05 40 :UNK.C4,C5,C6 :1-129 closest density 0.001

 

I repeated same calculation without the keyword closest. Results are
very different in closest as well as no closest. Also RDF does not
converge to 1. It becomes zero finally. I would like to understand why
RDF does not converge to 1, or how it normalize the values. I have
pasted the output (output_standard.xmgr) of these four runs for your
kind information.

 

I am looking forward for your suggestion and kind help.

 

Thanking you

 

Regards

 

Abdul Rajjak

 

 

        0.033 no closest

                0.033 closest

                        0.001 no closest

                        0.001 closest

        
bin

hist

occupancy

        

0.25

0

0

                0.25

0

0

                0.25

0

0

                0.25

0

0

0.75

0

0

                0.75

0

0

                0.75

0

0

                0.75

0

0

1.25

0

0

                1.25

0

0

                1.25

0

0

                1.25

0

0

1.75

0

0

                1.75

0

0

                1.75

0

0

                1.75

0

0

2.25

0

0

                2.25

0.002

0.003

                2.25

0

0

                2.25

0.079

0.003

2.75

0.001

0.001

                2.75

1.086

1.734

                2.75

0.019

0.001

                2.75

36.33

1.734

3.25

0.004

0.01

                3.25

4.972

12.794

                3.25

0.135

0.01

                3.25

166.337

12.794

3.75

0.009

0.038

                3.75

4.098

24.926

                3.75

0.317

0.038

                3.75

137.1

24.926

4.25

0.012

0.084

                4.25

2.397

34.039

                4.25

0.408

0.084

                4.25

80.202

34.039

4.75

0.014

0.15

                4.75

1.788

42.527

                4.75

0.466

0.15

                4.75

59.82

42.527

5.25

0.015

0.235

                5.25

1.311

50.126

                5.25

0.486

0.235

                5.25

43.845

50.126

5.75

0.016

0.346

                5.75

1.264

58.919

                5.75

0.535

0.346

                5.75

42.302

58.919

6.25

0.017

0.488

                6.25

1.14

68.286

                6.25

0.581

0.488

                6.25

38.143

68.286

6.75

0.019

0.672

                6.75

1.012

77.987

                6.75

0.64

0.672

                6.75

33.873

77.987

7.25

0.021

0.908

                7.25

0.851

87.397

                7.25

0.715

0.908

                7.25

28.482

87.397

7.75

0.023

1.202

                7.75

0.684

96.033

                7.75

0.778

1.202

                7.75

22.875

96.033

8.25

0.025

1.557

                8.25

0.582

104.367

                8.25

0.83

1.557

                8.25

19.482

104.367

8.75

0.026

1.982

                8.75

0.532

112.928

                8.75

0.884

1.982

                8.75

17.79

112.928

9.25

0.028

2.482

                9.25

0.49

121.737

                9.25

0.929

2.482

                9.25

16.382

121.737

9.75

0.029

3.056

                9.75

0.454

130.808

                9.75

0.962

3.056

                9.75

15.184

130.808

10.25

0.03

3.711

                10.25

0.434

140.384

                10.25

0.992

3.711

                10.25

14.504

140.384

10.75

0.031

4.453

                10.75

0.411

150.381

                10.75

1.021

4.453

                10.75

13.766

150.381

11.25

0.032

5.294

                11.25

0.403

161.102

                11.25

1.058

5.294

                11.25

13.48

161.102

11.75

0.033

6.245

                11.75

0.385

172.281

                11.75

1.097

6.245

                11.75

12.885

172.281

12.25

0.034

7.321

                12.25

0.35

183.326

                12.25

1.14

7.321

                12.25

11.712

183.326

12.75

0.035

8.527

                12.75

0.317

194.145

                12.75

1.181

8.527

                12.75

10.591

194.145

13.25

0.037

9.876

                13.25

0.288

204.758

                13.25

1.222

9.876

                13.25

9.62

204.758

13.75

0.038

11.37

                13.75

0.268

215.402

                13.75

1.258

11.37

                13.75

8.959

215.402

14.25

0.039

13.023

                14.25

0.248

225.976

                14.25

1.295

13.023

                14.25

8.287

225.976

14.75

0.04

14.838

                14.75

0.231

236.541

                14.75

1.328

14.838

                14.75

7.728

236.541

15.25

0.041

16.825

                15.25

0.21

246.802

                15.25

1.359

16.825

                15.25

7.022

246.802

15.75

0.041

18.985

                15.75

0.193

256.859

                15.75

1.386

18.985

                15.75

6.452

256.859

16.25

0.042

21.331

                16.25

0.171

266.347

                16.25

1.414

21.331

                16.25

5.718

266.347

16.75

0.043

23.871

                16.75

0.154

275.43

                16.75

1.441

23.871

                16.75

5.152

275.43

17.25

0.044

26.612

                17.25

0.138

284.078

                17.25

1.466

26.612

                17.25

4.625

284.078

17.75

0.045

29.559

                17.75

0.129

292.65

                17.75

1.489

29.559

                17.75

4.33

292.65

18.25

0.045

32.717

                18.25

0.122

301.174

                18.25

1.509

32.717

                18.25

4.073

301.174

18.75

0.046

36.093

                18.75

0.116

309.731

                18.75

1.528

36.093

                18.75

3.874

309.731

19.25

0.046

39.693

                19.25

0.109

318.191

                19.25

1.546

39.693

                19.25

3.633

318.191

19.75

0.047

43.523

                19.75

0.101

326.456

                19.75

1.563

43.523

                19.75

3.372

326.456

20.25

0.047

47.59

                20.25

0.095

334.647

                20.25

1.578

47.59

                20.25

3.179

334.647

20.75

0.048

51.902

                20.75

0.088

342.607

                20.75

1.594

51.902

                20.75

2.943

342.607

21.25

0.048

56.464

                21.25

0.081

350.343

                21.25

1.608

56.464

                21.25

2.726

350.343

21.75

0.048

61.279

                21.75

0.075

357.79

                21.75

1.62

61.279

                21.75

2.505

357.79

22.25

0.049

66.347

                22.25

0.069

364.948

                22.25

1.629

66.347

                22.25

2.301

364.948

22.75

0.049

71.673

                22.75

0.062

371.716

                22.75

1.638

71.673

                22.75

2.081

371.716

23.25

0.049

77.261

                23.25

0.057

378.185

                23.25

1.645

77.261

                23.25

1.905

378.185

23.75

0.049

83.119

                23.75

0.051

384.268

                23.75

1.653

83.119

                23.75

1.716

384.268

24.25

0.05

89.259

                24.25

0.045

389.889

                24.25

1.662

89.259

                24.25

1.521

389.889

24.75

0.05

95.691

                24.75

0.04

395.064

                24.75

1.671

95.691

                24.75

1.345

395.064

25.25

0.05

102.422

                25.25

0.034

399.674

                25.25

1.68

102.422

                25.25

1.151

399.674

25.75

0.05

109.457

                25.75

0.029

403.721

                25.75

1.689

109.457

                25.75

0.971

403.721

26.25

0.051

116.805

                26.25

0.024

407.172

                26.25

1.697

116.805

                26.25

0.797

407.172

26.75

0.051

124.467

                26.75

0.02

410.137

                26.75

1.704

124.467

                26.75

0.659

410.137

27.25

0.051

132.44

                27.25

0.016

412.669

                27.25

1.709

132.44

                27.25

0.543

412.669

27.75

0.051

140.724

                27.75

0.013

414.748

                27.75

1.712

140.724

                27.75

0.43

414.748

28.25

0.051

149.316

                28.25

0.011

416.552

                28.25

1.714

149.316

                28.25

0.36

416.552

28.75

0.051

158.219

                28.75

0.008

418.014

                28.75

1.714

158.219

                28.75

0.282

418.014

29.25

0.051

167.428

                29.25

0.007

419.236

                29.25

1.713

167.428

                29.25

0.227

419.236

29.75

0.051

176.911

                29.75

0.005

420.256

                29.75

1.705

176.911

                29.75

0.183

420.256

30.25

0.05

186.532

                30.25

0.005

421.123

                30.25

1.673

186.532

                30.25

0.151

421.123

30.75

0.049

196.28

                30.75

0.004

421.836

                30.75

1.641

196.28

                30.75

0.12

421.836

31.25

0.048

206.148

                31.25

0.003

422.362

                31.25

1.608

206.148

                31.25

0.086

422.362

31.75

0.047

216.042

                31.75

0.002

422.711

                31.75

1.562

216.042

                31.75

0.055

422.711

32.25

0.045

225.899

                32.25

0.001

422.896

                32.25

1.508

225.899

                32.25

0.028

422.896

32.75

0.044

235.71

                32.75

0

422.974

                32.75

1.456

235.71

                32.75

0.012

422.974

33.25

0.042

245.472

                33.25

0

422.992

                33.25

1.405

245.472

                33.25

0.003

422.992

33.75

0.041

255.173

                33.75

0

422.998

                33.75

1.355

255.173

                33.75

0.001

422.998

34.25

0.039

264.802

                34.25

0

423

                34.25

1.306

264.802

                34.25

0

423

34.75

0.038

274.353

                34.75

0

423

                34.75

1.259

274.353

                34.75

0

423

35.25

0.036

283.817

                35.25

0

423

                35.25

1.212

283.817

                35.25

0

423

35.75

0.035

293.097

                35.75

0

423

                35.75

1.156

293.097

                35.75

0

423

36.25

0.032

302.069

                36.25

0

423

                36.25

1.087

302.069

                36.25

0

423

36.75

0.031

310.73

                36.75

0

423

                36.75

1.021

310.73

                36.75

0

423

37.25

0.029

319.081

                37.25

0

423

                37.25

0.958

319.081

                37.25

0

423

37.75

0.027

327.111

                37.75

0

423

                37.75

0.897

327.111

                37.75

0

423

38.25

0.025

334.815

                38.25

0

423

                38.25

0.838

334.815

                38.25

0

423

38.75

0.023

342.188

                38.75

0

423

                38.75

0.781

342.188

                38.75

0

423

39.25

0.022

349.226

                39.25

0

423

                39.25

0.727

349.226

                39.25

0

423

39.75

0.02

355.923

                39.75

0

423

                39.75

0.675

355.923

                39.75

0

423

 

 

 

 

 

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Received on Tue Feb 23 2010 - 00:30:02 PST
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