[gmx-users] fitting problem

[Mark Abraham]

On Sun, Nov 16, 2014 at 9:08 PM, Rohit Farmer <rohit.farmer at gmail.com>
wrote:

> Hi there,
>
> I am trying to fit a protein to a reference structure using the command
> below
>
> trjconv -s run.trp -f run.xtc -o run-fit.xtc -fit progressive
>

Please copy and paste your actual command. Not what you think it was +
typos + whatever changes you don't think matter :-).


>
> I am using protein for least square and system for output.
>
> This command always worked for me but for this particular protein the side
> chains get crooked. I don't know how to explain but they look like flat
> structures with random bonds between the atoms.
>

So take a screenshot, upload to a file-sharing service and share the link.


> I tried -pbc mol and whole instead of fit just to get rid of the pbc effect
> and don't care about fitting. But it also gave the same result.
>

Then you may be trying to fit files whose topology atom ordering does not
match, or something like that. Note that if the molecules aren't whole in
the .tpr file, then you won't be doing anything useful with some of the
-pbc options.

Mark


> Can someone please help.
>
> Thanks
>
> Rohit
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