AMBER Archive (2005)

Subject: Re: AMBER: restart coordinate file

From: s0344557_at_sms.ed.ac.uk
Date: Thu Nov 10 2005 - 10:11:49 CST

Thanks very much Bill and Carlos. Surely there is not velocity in the
trajectory
file. I neglect such an obvious problem. Now I think I could sort it out.

Lan

Quoting Bill Ross <ross_at_cgl.ucsf.edu>:

>> 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.
>
> By the way, carnal is going to be dropped from amber, so you
> may want to start getting familiar with ptraj.
>
>> ...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?
>
> You cannot get velocities from mdcrd because it does not contain
> them. If you saved mdvel at the same interval, you could extract
> the corresponding set of velocities using the same method (since
> the file format is the same), and then manually create a restrt
> by combining coords & velocities for frame 134 using an editor.
>
> The box info may not be in the mdcrd either - look at the file and
> see.. if it is, then there is a carnal bug in not transferring it
> to the new restrt. Since carnal won't be fixed (unless someone
> likes it enough to take over maintenance), you would have to do
> this manually or switch to ptraj. If there is no box info (this
> might happen w/ constant volume, not sure), then you would have
> to get the box from somewhere else and add it manually.
>
> Bill
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