On 10/29/12 9:59 AM, Albert wrote:
On 10/28/2012 09:06 PM, Justin Lemkul wrote:
Visual inspection with a text editor should tell you what's wrong. Either the
file is incomplete (i.e. header or box vectors missing) or the coordinates are
large (indicating the system became unstable at some point). The fact that
VMD loads the file suggests that the latter may be true. An incomplete file
would not load, but one with screwy coordinates still would.
-Justin
--
Hello Justin:
thanks a lot for kind advices.
I check the file with gedit and I didn't find anything unusual within the text
comparing with the original .gro file. They have the exact the same row and
columns.
Generated by trjconv : MOR t= 116.00
Generated by trjconv : MOR t= 1160000.00000
You shouldn't have two separate title lines. I don't know how trjconv would
have produced garbled output like this, but I suspect it's the cause of your
problems.
-Justin
48328
65MET N 1 4.934 1.182 7.535 0.0471 0.2110 0.3278
65MET HT1 2 4.975 1.148 7.620 -2.1539 -2.5438 0.4303
65MET HT2 3 4.879 1.108 7.497 0.2031 0.2641 -0.0060
65MET CA 4 5.035 1.229 7.441 -0.1568 -0.5819 -0.2954
65MET HA 5 5.090 1.312 7.481 2.2845 -1.6076 -1.3193
65MET CB 6 5.149 1.126 7.437 0.4809 0.1027 0.0700
65MET HB1 7 5.166 1.099 7.544 -2.2162 1.7701 1.0201
65MET HB2 8 5.117 1.032 7.386 -3.2381 0.4514 1.4551
65MET CG 9 5.283 1.173 7.379 0.1733 0.3849 -0.4145
65MET HG1 10 5.340 1.078 7.384 0.4424 0.6052 2.0263
.
.
.
9511CL CL48320 2.101 1.980 2.259 0.0337 -0.1667 0.2316
9512CL CL48321 4.165 3.237 10.196 -0.4009 0.1697 0.4481
9513CL CL48322 5.414 4.564 9.686 -0.1624 -0.0698 -0.2503
9514CL CL48323 2.032 1.126 1.460 0.0876 -0.4133 -0.1336
9515CL CL48324 3.278 3.994 9.006 0.1073 -0.1139 0.6701
9516CL CL48325 1.793 3.569 9.888 0.0911 0.2208 -0.0272
9517CL CL48326 1.046 2.735 1.322 0.1044 0.2204 0.4059
9518CL CL48327 3.384 4.016 1.983 0.0078 0.1266 -0.1903
9519CL CL48328 0.044 3.730 0.932 -0.2059 0.0577 0.3350
6.69862 6.69862 10.42296
thank you very much
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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