AMBER Archive (2006)

Subject: RE: AMBER: Post-MD minimization

From: sangeeta_at_bioinfo.ernet.in
Date: Fri Jun 23 2006 - 01:09:31 CDT

Dear Amber Community,
Prof. Walker gave useful hints to my queries reg. the MD trajectory
minimization. Now I have two comments about the same issue.

On Mon, 19 Jun 2006, Ross Walker wrote:

> > 2. I would like to get the coordinates of the minimzed
> > structures. How do
> > I specify this in the sander.MPI command? B'se with reference to the
> > previous discussions on AMBER reflector, -x is the flag for
> > reading in the
> > trajectory file. I also checked the trajene files of the test
> > set provided
> > with AMBER. In this set also, I could not figure out where
> > the minimized
> > structrues are stored. In the minimiztion run that I am
> > doing, even the
> > .rst file has not been created.
>
> The coordinates from a minimization get written to the restart file as
> specified with the -r flag so in your case:
>
> mpirun -np 4 $AMBERHOME/exe/sander.MPI -O -i cga_gb_fnl_min.in -p
> ../../prmtop -o cga_gb_fnl_min.out -c ../cga_gb_prod10ns.rst -x
> ../cga_gb_prod10ns_trj.crd -r cga_gb_10ns_fmin.rst > out_cga_gb_fnl_min
>
> cga_gb_10ns_fmin.rst which if you use the same name for all 10,000
> minimisations just gets overwritten on every run such that you only have the
> coordinates for the last calculation that ran. it is probably blank because
> the run is still in progress when you looked at it. (-x is not required in
> minimization)

  I did carry out the entire minimization with the above parameters
but the .rst file never got created! I am unable to understand why. I got
only the *.out file.

>
> Note also that by specifying -c ../cga_gb_prod10ns.rst as the input
> structure for the minimisation, assuming you used the same rst structure for
> each case you will have successfully run the same minimisation 10,000
> times... There is no function to read the coordinate file in minimisation.

But, it is mentioned in the manual that setting IMIN = 5, Sander expects a
trajectory (.crd) file as an input and also that -y flag can be used to
specify this inpcrd file (page 87 as well as page 90 of the manual).
However, if the -y flag is used, it results in an error that the flag is
not a valid one. (This has been discussed in some of the earlier
discussions on the AMBER reflector as well. At that time it was suggested
that -x should be used for specifying the imput trajectory coordinates.)

Moreover, there should be a provision with these settings to save **all**
the minimized coordinates as this option may be used like a batch
minimization of several captures structures. Right now only -r option is
available for the output coordinates. Is there any such provision which I
have missed?

>
> You will need to use ptraj to split your mdcrd file into 10,000 sequentially
> numbered rst files. You will then need to script the running of your
> minimisation such that each run picks the next sequentially numbered input
> rst file and writes a unique (probably sequential) -r rst file on each run.
> You can then post process all these rst files produced from the minimisation
> in ptraj or ambpdb to obtain pdb files if you need them.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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