Dear Amber,
I want to extract a particular snapshots (rst file) from the trajectory and then use it as a input file for umbrella sample calculation.
I do this according to the several topic in Amber,
http://archive.ambermd.org/201303/0382.html
http://archive.ambermd.org/201711/0236.html
http://archive.ambermd.org/201501/0224.html
trajin input.nc
trajout output.rst7 restart onlyframes 10,18,27
The rst files were generated successfully, but it can not display in VMD, I compared the generated rst file and the rst file generated from the molecular dynamic (it can display in VMD),and find the later has some additional data at the end of section like this,
...........................................
19.1857051 -4.6555116 7.4146023 18.8220371 -5.3773736 6.9018717
18.4637523 -4.3729673 7.9760155 -2.4243654 -13.8058101 -21.2786187
-1.9146608 -14.5002933 -21.6959029 -2.8608247 -13.3598833 -22.0044868
-21.2150809 6.2174653 8.4211042 -20.7638532 6.7598422 9.0679834
-20.6390472 6.2272326 7.6566948 24.7070281 21.5076812 1.1709882
25.4433883 20.9042852 1.0713951 24.3839246 21.3469960 2.0575638
0.2912960 0.3037410 0.0134569 -0.1705091 -0.5272947 0.0271020
0.4082844 0.0781819 0.5481728 0.2932252 0.3393415 -0.6883875
-0.1237484 -0.4178922 0.9020592 1.3871243 0.2444639 -0.9532233
0.2631257 -0.6038555 -0.2920701 0.6753066 -0.3941904 1.2131384
0.2149299 0.0004143 0.4132927 0.2765796 -0.6031886 0.6400029
0.3344137 0.4029519 0.2140909 -0.3032180 -0.0292121 -0.0483147
-0.2182475 0.2596782 0.4890635 0.2202241 -0.4463871 0.0644583
0.2769499 -0.0245921 0.0969901 -0.2766073 -0.2109181 -0.2420671
................................
How can I generated the rst file correctly and display in VMD.
I will be much appreciate if there are any sugesstion.
Zhihong Xin
Nanjing Agricultural University
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Received on Wed Jan 27 2021 - 20:30:02 PST
