the trajectory file does not include velocities so
there is no way to extract it. I suggest using ntx=1
and reassigning velocities for the restart.
ptraj also does restart writing well, you dn't need to use
carnal.
s0344557.sms.ed.ac.uk wrote:
>Dear AMBER users,
>
>I am trying to pick up a certain structure from a MD trajectory file to work as
>a restart file for the next round refinement calculation. Let's say I have got
>200 frames in the trajectory and I want to get the restart file using the
>number 134 frame. The following are my input of carnal input file.
>
>
>FILES_IN
> PARM p1 prm.top;
> STREAM s1 mdcrd.prod4;
>
>FILES_OUT
> COORD c1 temp.rst RST;
>DECLARE
>
>OUTPUT
> COORD c1 s1 SELECT (134);
>END
>
>But the ouput file 'temp.rst.134' does not have the velocity and the box
>information. There is only xyz coordinates in it. And it is cannot be used for
>the next round of calculation. Could anybody give me some clue how I can get a
>correct restart file for a certain frame from the trajectory file? Many thanks
>in advance.
>
>Cheers,
>Lan
>
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Received on Thu Nov 10 2005 - 15:53:01 PST
