[gmx-users] Structure averaging problem using g_rmsf

[Justin A. Lemkul]

Spring buds wrote:
> Hi
> 
> I am trying to average the structure from the last 10ns from 100ns. So I 
> used the command which is below:
> 
> g_rmsf –f 100.xtc –s topol.tpr –b 90001 –e 100000 –ox traj_avg.pdb
> 
> But I got below error: 
> 
> "Program g_rmsf, VERSION 4.5.4
> Source code file: /root/Desktop/gromacs-4.5.4/src/gmxlib/trxio.c, line: 713
> 
> Fatal error:
> Specified frame doesn't exist or file not seekable"
> 

You're specifying a frame that doesn't exist, either 90001 or 100000.  Likely 
90001 is not an actual time in the trajectory, thus giving rise to the "not 
seekable" error.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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