Hello,
I used the following leap.in file to prepare protein solvated into a water
box, and min.in to minimize protein structure together with water box. The
problem here is that, when I set "ntb = 0" (no periodic boundary) in min.in,
everything works fine. However, when I set "ntb = 1", min.out is empty
(containing nothing), no min.rst is generated and the program terminates
quick. Does someone have any idea on this? Thanks a lot!
*leap.in*
1. source leaprc.ff99SB
2. set default pbradii bondi
3. loadOff ions.lib
4. loadamberparams frcmod.ions
5. com = loadpdb 1POD.pdb0
6. solvatebox com TIP3PBOX 12.0
7. saveamberparm com pla2.top pla2.crd
8. savepdb com pla2.pdb
9. quit
*
min.in
*
l. minimize pla2-ca
2. &cntrl
3. imin=1,maxcyc=1000,ncyc=500,
4. cut=8.0,ntb=1,
5. ntc=2,ntf=2,
6. ntpr=100,
7. ntr=1, restraint_wt=2.0,
8. restraintmask=':1-120',
9. /
Xue
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Received on Sun Sep 19 2010 - 08:30:03 PDT
