AMBER Archive (2006)

Subject: Re: AMBER: (no subject)

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Tue Aug 15 2006 - 07:51:49 CDT

> It is the ptraj file that I used to calculate rmsd,
>
> ===============================================
> trajin jta.mdcrd
> trajout jta_ptraj.mdcrd
> rms first out jta_linker_nocenter.rmsfit :436-511,512 time 0.50
> ================================================
>
> Then I type
>
> ====================
> ptraj jta.prmtop < jta.ptraj
> ====================
>
> ================================================
> Processing AMBER trajectory file 1K4T_aCPT4_md2.mdcrd ( ?)
>
The processing trajectory should be jta.mdcrd according to your input,
you need to check your current directroy, from here I can say maybe you
are using the script to make input jta.ptraj, so you can first delete
the previous jta.ptraj and then run your script.

> Set 1 .................................................
> Set #50 appears corrupted (
> 22.681 -8.543 27.3283)
>
>
> PTRAJ: Successfully read in 49 sets and processed 49 sets.
> Dumping accumulated results (if any)
>
So, the error came from different number of coordinates and atom. You
should care about this error. The ptraj takes the three coordinates
means three values from the trajectory file for each atom consecutively,
so the number of coordinates should be equal to the three times the
number of atoms in each frame.

navnit
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