$ambpdb -p prmtop < prmcrd > output.pdb
You can then use some program such as babel to translate file formats or
use tleap to do this
Eddie
Mehmet Serkan Apaydin wrote:
> Hello,
>
> I have an input structure that I would like to energy minimize and
> compute its energy. In the Amber9 tutorial in p. 13, there is a short
> introduction on how to minimize the energy of an input structure,
> however the output of the sander program is in the .xyz format. I was
> wondering how to convert the result of the minimization into a pdb
> format. I understand that after minimization the energy can be
> fetched from the intermediate results file.
>
> For reference, here is the tleap script:
> source leaprc.ff03
> ef1 = loadPdb 1EF1-NMA.7.model1.pdb
> saveAmberParm ef1 prmtop prmcrd
> quit
>
> and here is the sander script min.in:
> # 200m steps of minimization, generalized Born solvent model
> &cntrl
> maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
> /
>
> And sander is run with the following command:
>
> sander -i min.in -o 1ef1.min1.out -c prmcrd -r 1ef1.min1.xyz
>
> Thanks,
>
> --Serkan
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Received on Wed Nov 21 2007 - 06:07:42 PST
