Hi amber users,
I am analysing a trajectory spanning 1860ps divided into 11 stages. My input ptraj script to calculate RMSd is as shown below, (THERE WAS NO LINE BREAK AT THE .CA POINT) and it worked fine when I worked with a first equilibrium 20ps run. When I run this script, I only get RMSd values for 479.6 out of the 1860ps trajectory, and when I tried to run a similar script with a similar trajectory with the same time span the RMSd values got dumped over 720ps. Can anyone tell me why this happens please? The only error message I get is the following:
ERROR in dispatchToken: Token string "undocked_calc_backbone_rms.in" not
found in tokenlist
but then all seems to proceed as normal....
PTRAJ: Successfully read in 2398 sets and processed 2398 sets.
Dumping accumulated results (if any)
PTRAJ RMS: dumping RMSd vs time data
Thanks
Claire
undocked_calc_backbone_rms.in
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md2.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md3.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md4.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md5.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md6.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md7.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md8.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md9.mdcrd.gz
trajin /DATA/VINCLOZOLIN_DYNAMICS/1e3g_Vinclozolin_S_docked_md10.mdcrd.gz
rms first out
/DATA/VINCLOZOLIN_TRAJECTORY_ANALYSIS/vinclozolin_backbone.rms .CA time 0.2
strip :WAT
go
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Received on Wed May 24 2006 - 06:07:10 PDT
