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.CA,C,N,O' out rms7-88.dat
vector r2 :2.N corr :2.H
vector r3 :3.N corr :3.H
vector r4 :4.N corr :4.H
vector r5 :5.N corr :5.H
vector r6 :6.N corr :6.H
vector r7 :7.N corr :7.H
vector r8 :8.N corr :8.H
vector r9 :9.N corr :9.H
vector r10 :10.N corr :10.H
vector r11 :11.N corr :11.H
vector r12 :12.N corr :12.H
vector r13 :13.N corr :13.H
vector r14 :14.N corr :14.H
vector r15 :15.N corr :15.H
vector r16 :16.N corr :16.H
vector r17 :17.N corr :17.H
vector r18 :18.N corr :18.H
vector r19 :19.N corr :19.H
vector r20 :20.N corr :20.H
vector r21 :21.N corr :21.H
vector r22 :22.N corr :22.H
vector r23 :23.N corr :23.H
vector r24 :24.N corr :24.H
vector r25 :25.N corr :25.H
vector r26 :26.N corr :26.H
vector r27 :27.N corr :27.H
vector r28 :28.N corr :28.H
vector r29 :29.N corr :29.H
vector r30 :30.N corr :30.H
vector r31 :31.N corr :31.H
vector r32 :32.N corr :32.H
vector r33 :33.N corr :33.H
vector r34 :34.N corr :34.H
vector r35 :35.N corr :35.H
vector r36 :36.N corr :36.H
vector r37 :37.N corr :37.H
vector r38 :38.N corr :38.H
vector r39 :39.N corr :39.H
vector r40 :40.N corr :40.H
vector r41 :41.N corr :41.H
vector r42 :42.N corr :42.H
vector r43 :43.N corr :43.H
vector r44 :44.N corr :44.H
vector r45 :45.N corr :45.H
vector r46 :46.N corr :46.H
vector r47 :47.N corr :47.H
vector r48 :48.N corr :48.H
vector r49 :49.N corr :49.H
vector r50 :50.N corr :50.H
vector r51 :51.N corr :51.H
vector r52 :52.N corr :52.H
vector r53 :53.N corr :53.H
vector r54 :54.N corr :54.H
vector r55 :55.N corr :55.H
vector r56 :56.N corr :56.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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Received on Sun Nov 11 2007 - 06:07:35 PST
