AMBER Archive (2007)

Subject: Re: AMBER: How can i calculate generalized order parameters using ptraj.

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 08 2007 - 20:23:34 CST

On Sun, Oct 28, 2007, cgji wrote:
>
> I want to calculate generalized order parameters of each amino acid
> residues (N-H vector) by molecular dynamics simulation.
> And compare it to order parameters derived from NMR experiment .
>
> It seems that ptraj support two methods suitable for calculating order
> parameters from dynamic trajectory .
> One method calculate it directly from Legendre polynomial .
> Ane the other one calculate it using iRED technique .
>
> >From the amber9 manual , I know some key words related to such analysis.
> >(VECTOR , MATRIX ,ANALYZE MATRIX)
>
> However , i don't know how to carry out such analysis exactly.

Attached is a ptraj input script I have used for a small protein. You should
be able to adapt this to your problem.

...good luck...dac

trajin eq7-88.prot2.trj.gz
reference ../igb1/eq0.x
rms reference ':3-54_at_CA,C,N,O' out rms7-88.dat

vector r2 :2_at_N corr :2_at_H
vector r3 :3_at_N corr :3_at_H
vector r4 :4_at_N corr :4_at_H
vector r5 :5_at_N corr :5_at_H
vector r6 :6_at_N corr :6_at_H
vector r7 :7_at_N corr :7_at_H
vector r8 :8_at_N corr :8_at_H
vector r9 :9_at_N corr :9_at_H

vector r10 :10_at_N corr :10_at_H
vector r11 :11_at_N corr :11_at_H
vector r12 :12_at_N corr :12_at_H
vector r13 :13_at_N corr :13_at_H
vector r14 :14_at_N corr :14_at_H
vector r15 :15_at_N corr :15_at_H
vector r16 :16_at_N corr :16_at_H
vector r17 :17_at_N corr :17_at_H
vector r18 :18_at_N corr :18_at_H
vector r19 :19_at_N corr :19_at_H

vector r20 :20_at_N corr :20_at_H
vector r21 :21_at_N corr :21_at_H
vector r22 :22_at_N corr :22_at_H
vector r23 :23_at_N corr :23_at_H
vector r24 :24_at_N corr :24_at_H
vector r25 :25_at_N corr :25_at_H
vector r26 :26_at_N corr :26_at_H
vector r27 :27_at_N corr :27_at_H
vector r28 :28_at_N corr :28_at_H
vector r29 :29_at_N corr :29_at_H

vector r30 :30_at_N corr :30_at_H
vector r31 :31_at_N corr :31_at_H
vector r32 :32_at_N corr :32_at_H
vector r33 :33_at_N corr :33_at_H
vector r34 :34_at_N corr :34_at_H
vector r35 :35_at_N corr :35_at_H
vector r36 :36_at_N corr :36_at_H
vector r37 :37_at_N corr :37_at_H
vector r38 :38_at_N corr :38_at_H
vector r39 :39_at_N corr :39_at_H

vector r40 :40_at_N corr :40_at_H
vector r41 :41_at_N corr :41_at_H
vector r42 :42_at_N corr :42_at_H
vector r43 :43_at_N corr :43_at_H
vector r44 :44_at_N corr :44_at_H
vector r45 :45_at_N corr :45_at_H
vector r46 :46_at_N corr :46_at_H
vector r47 :47_at_N corr :47_at_H
vector r48 :48_at_N corr :48_at_H
vector r49 :49_at_N corr :49_at_H

vector r50 :50_at_N corr :50_at_H
vector r51 :51_at_N corr :51_at_H
vector r52 :52_at_N corr :52_at_H
vector r53 :53_at_N corr :53_at_H
vector r54 :54_at_N corr :54_at_H
vector r55 :55_at_N corr :55_at_H
vector r56 :56_at_N corr :56_at_H

analyze timecorr vec1 r2 vec2 r2 out r02.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r3 vec2 r3 out r03.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r4 vec2 r4 out r04.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r5 vec2 r5 out r05.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r6 vec2 r6 out r06.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r7 vec2 r7 out r07.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r8 vec2 r8 out r08.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r9 vec2 r9 out r09.nh tcorr 10000. tstep 2.0

analyze timecorr vec1 r10 vec2 r10 out r10.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r11 vec2 r11 out r11.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r12 vec2 r12 out r12.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r13 vec2 r13 out r13.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r14 vec2 r14 out r14.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r15 vec2 r15 out r15.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r16 vec2 r16 out r16.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r17 vec2 r17 out r17.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r18 vec2 r18 out r18.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r19 vec2 r19 out r19.nh tcorr 10000. tstep 2.0

analyze timecorr vec1 r20 vec2 r20 out r20.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r21 vec2 r21 out r21.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r22 vec2 r22 out r22.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r23 vec2 r23 out r23.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r24 vec2 r24 out r24.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r25 vec2 r25 out r25.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r26 vec2 r26 out r26.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r27 vec2 r27 out r27.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r28 vec2 r28 out r28.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r29 vec2 r29 out r29.nh tcorr 10000. tstep 2.0

analyze timecorr vec1 r30 vec2 r30 out r30.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r31 vec2 r31 out r31.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r32 vec2 r32 out r32.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r33 vec2 r33 out r33.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r34 vec2 r34 out r34.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r35 vec2 r35 out r35.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r36 vec2 r36 out r36.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r37 vec2 r37 out r37.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r38 vec2 r38 out r38.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r39 vec2 r39 out r39.nh tcorr 10000. tstep 2.0

analyze timecorr vec1 r40 vec2 r40 out r40.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r41 vec2 r41 out r41.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r42 vec2 r42 out r42.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r43 vec2 r43 out r43.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r44 vec2 r44 out r44.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r45 vec2 r45 out r45.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r46 vec2 r46 out r46.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r47 vec2 r47 out r47.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r48 vec2 r48 out r48.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r49 vec2 r49 out r49.nh tcorr 10000. tstep 2.0

analyze timecorr vec1 r50 vec2 r50 out r50.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r51 vec2 r51 out r51.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r52 vec2 r52 out r52.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r53 vec2 r53 out r53.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r54 vec2 r54 out r54.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r55 vec2 r55 out r55.nh tcorr 10000. tstep 2.0
analyze timecorr vec1 r56 vec2 r56 out r56.nh tcorr 10000. tstep 2.0

go
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