AMBER Archive (2006)

Subject: AMBER: Distance between two atoms

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Tue Oct 03 2006 - 18:59:17 CDT

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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