[gmx-users] Trjconv error

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 19 08:30:47 CEST 2012

On 19/06/2012 4:13 PM, Shima Arasteh wrote:
> Dear gmx users,
> I want to follow the workflow regarding to
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> for the second step I enter the command as below:
> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
> But I get the error:
>   Index[232] 235 is larger than the number of atoms in the
> trajectory file (234). There is a mismatch in the contents
> of your -f, -s and/or -n files
> I don't have any index file, so what this error is talking about?

Then it must mean there's a mismatch in the contents of your -f and -s 
files... each must refer to the same system. Something about your past 
management of these two files makes your intended operation a nonsense, 
but we can't know what. If, for example, you chose xtcgroups in your 
.mdp file as something other than System, then they do not.


>   How may I solve it? Anybody may suggest me any solution please?
>  I would be so thankful for your suggestions.
> Sincerely,
> Shima

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