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
