AMBER: newby question on converting xyz format to pdb format after energy minimization

From: Mehmet Serkan Apaydin <apaydin.cs.duke.edu>
Date: Tue, 20 Nov 2007 16:02:42 -0500

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
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