AMBER Archive (2006)

Subject: AMBER: Re: Distance between two atoms

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Oct 04 2006 - 01:12:06 CDT

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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