AMBER Archive (2006)

Subject: Re: AMBER: RMSd error

From: Carlos Simmerling (
Date: Mon May 22 2006 - 07:02:02 CDT

it looks like that "undocked..." line should not be there, is it a title?
concerning the # of RMSD values, I don't know what could be
wrong, I always get the same number that ptraj says it is writing.
this is 2398 values - do you get that? you say it is 1860ps but
I don't know how many frames should be in the files.
look at the ptraj output for each of the files, it will tell you how
many frames it found in the trajectory. check that against
what you think should be there and narrow it down to
perhaps 1 file that doesn't match. you have so many files
in this run that it is harder to debug.

Claire Zerafa wrote:

> 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 "" 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
> 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
> time 0.2
> strip :WAT
> go

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