AMBER Archive (2006)

Subject: Re: AMBER: Re: Distance between two atoms

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Oct 04 2006 - 01:41:27 CDT

For the specified distance between 2 atoms, I use
MOLMOL to measure it. Can we say that the MolMol and
Ptraj have different strategy to calculate the
distance between the same pair of atoms?

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

--- Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:

> What should I mention here is that the last rst file
> has a specified distance shorter than 2. However in
> the excell table the last snapshop has the specified
> distance higher than 2.0 A.
>
> Any comments and discussion on it will welcome.
>
> Best regards.
>
> Fenghui Fan
>
> --- Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:
>
> > Dear all,
> >
> > I have a mdcrd file. When I transfer the .rst file
> > to
> > the pdb file, the PDB will will be:
> >
> > .....
> >
> > ATOM 1187 N ARG 79 27.112 27.770
> > 39.171
> > ATOM 1188 H ARG 79 26.317 27.600
> > 38.572
> > ATOM 1189 CA ARG 79 27.674 29.157
> > 39.104
> > ATOM 1190 HA ARG 79 28.757 29.044
> > 39.070
> > ATOM 1191 CB ARG 79 27.115 29.913
> > 37.893
> > ATOM 1192 2HB ARG 79 26.039 30.062
> > 37.984
> > ATOM 1193 3HB ARG 79 27.632 30.860
> > 37.739
> > ATOM 1194 CG ARG 79 27.230 29.195
> > 36.537
> > ATOM 1195 2HG ARG 79 26.648 28.276
> > 36.458
> > ATOM 1196 3HG ARG 79 26.814 29.946
> > 35.865
> > ATOM 1197 CD ARG 79 28.769 28.912
> > 36.206
> > ATOM 1198 2HD ARG 79 29.343 29.819
> > 36.399
> > ATOM 1199 3HD ARG 79 29.052 28.143
> > 36.925
> > ATOM 1200 NE ARG 79 29.044 28.428
> > 34.854
> > ATOM 1201 HE ARG 79 28.254 28.454
> > 34.226
> > ATOM 1202 CZ ARG 79 30.174 28.118
> > 34.363
> > ATOM 1203 NH1 ARG 79 31.230 28.026
> > 35.068
> > ATOM 1204 1HH1 ARG 79 31.200 28.539
> > 35.937
> > ATOM 1205 2HH1 ARG 79 32.178 27.915
> > 34.736
> > ATOM 1206 NH2 ARG 79 30.335 27.942
> > 33.088
> > ATOM 1207 1HH2 ARG 79 29.622 28.324
> > 32.484
> > ATOM 1208 2HH2 ARG 79 31.278 27.861
> > 32.737
> > ATOM 1209 C ARG 79 27.440 29.895
> > 40.410
> > ATOM 1210 O ARG 79 26.318 29.824
> > 40.980
> >
> > --------
> > ATOM 2082 O2* CMP 134 34.548 33.551
> > 37.320
> > ATOM 2083 HAA CMP 134 35.214 32.840
> > 37.332
> > ATOM 2084 C2* CMP 134 34.102 33.622
> > 38.675
> > ATOM 2085 1H2* CMP 134 34.896 33.447
> > 39.406
> > ATOM 2086 C3* CMP 134 32.890 32.712
> > 38.860
> > ATOM 2087 1H3* CMP 134 32.810 32.648
> > 39.948
> > ATOM 2088 O3* CMP 134 32.902 31.433
> > 38.222
> > ATOM 2089 P CMP 134 31.534 30.568
> > 38.289
> > ATOM 2090 O1P CMP 134 31.605 29.306
> > 37.535
> > ATOM 2091 O2P CMP 134 30.986 30.215
> > 39.632
> > ATOM 2092 O5* CMP 134 30.485 31.602
> > 37.666
> > ATOM 2093 C5* CMP 134 30.338 32.862
> > 38.318
> > ATOM 2094 1H5* CMP 134 30.103 32.658
> > 39.365
> > ATOM 2095 2H5* CMP 134 29.523 33.471
> > 37.918
> > ATOM 2096 C4* CMP 134 31.743 33.563
> > 38.279
> > ATOM 2097 1H4* CMP 134 31.960 33.761
> > 37.226
> > ATOM 2098 O4* CMP 134 31.965 34.825
> > 38.936
> > ATOM 2099 C1* CMP 134 33.436 35.011
> > 38.915
> > ATOM 2100 1H1* CMP 134 33.693 35.585
> > 38.012
> > ATOM 2101 N9 CMP 134 33.955 35.777
> > 40.063
> > ATOM 2102 C8 CMP 134 34.705 36.948
> > 40.009
> > ATOM 2103 1H8 CMP 134 34.762 37.594
> > 39.146
> > ATOM 2104 N7 CMP 134 35.390 37.155
> > 41.105
> > ATOM 2105 C5 CMP 134 35.080 36.006
> > 41.792
> > ATOM 2106 C4 CMP 134 34.110 35.215
> > 41.251
> > ATOM 2107 N3 CMP 134 33.724 34.079
> > 41.916
> > ATOM 2108 C2 CMP 134 34.289 33.796
> > 43.112
> > ATOM 2109 1H2 CMP 134 34.097 32.781
> > 43.443
> > ATOM 2110 N1 CMP 134 35.270 34.527
> > 43.641
> > ATOM 2111 C6 CMP 134 35.576 35.654
> > 43.026
> > ATOM 2112 N6 CMP 134 36.534 36.298
> > 43.639
> > ATOM 2113 HAC CMP 134 37.156 35.591
> > 44.015
> > ATOM 2114 HAB CMP 134 36.882 36.841
> > 42.857
> > ------------------
> >
> > I want to calculate the distance of :79_at_1HH1 &
> > :134_at_O1P
> >
> > As I know, at least there are some PDB files from
> > different period of md interval can give the
> > distance
> > shorter than 2 A.
> >
> > However, when I use the ptraj to get the distance:
> >
> > trajin complex_md1.mdcrd
> > trajin complex_md2.mdcrd
> > distance DIST :79_at_1HH1 :134_at_O1P out
> >
>
1015000cAMP_cAMPCOMPLEX_INTERHBOND_ARG79NH11_CMPO1PMOD.dat
> >
> > and I used excell to get the curve of distance vs
> > time.
> >
> > To my surpriae, in the curve all the distance is
> > longer than 2 A.
> >
> > Will you please tell mw what cau cause this
> > inconsistency?
> >
> > I am looking forward to getting your reply.
> >
> > Best regards.
> >
> > Fenghui Fan
> >
> >
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>
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