> Dear Amber users,
> I executed it for checkoverlap .It gives the output,specifying the atoms
> that are closest by that distance . Is it possible to calculate it by
> residue .I tried to dump my output to a file , but it does not work .Can
> anybody show where I am going wrong in my script.
>
> I used Amber tools (ptraj) ,checkoverlap to get the number of residues
> clustering at a particular frame of my trajectory file (i.e within a
> distance of 1 Angstorm ) .No output file was generated .
>
trajin trajectory.x 1000 1000
checkoverlap :1,2,3,4,5 min 1.0 around :1,2,3,4,5 out file.dat
I appreciate your suggestions.
Thanks
John
>
> For example if I have 5 residues
>
> trajin trajectory.x 1000 1000
> checkoverlap :1,2,3,4,5 min 1.0 around :1,2,3,4,5
>
> What is the format of output file for this tool and where should I specify
> it .
> I would also like to know whether this is the suitable tool to know the
> clustering of residues .
> Your suggestion are highly appreciated .
>
> Thanks
> John
>
>
>
>
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 18 2010 - 13:00:04 PDT
