Dear sir :
I am simulating a Molecular Crystal by AmberTools 1.5 & Amber 11. I established a pdb of supercell sucessfully by methods in Amber turials . In the next step , I want to minimize the supercell under periodic conditions, but I found that I can't estabilish a reasonable periodic boundary condition.
In these problems ,the first one is that not all angle parameters of crystal are 90 so that we can't establish a reasonable Triclinic box expect Cubic box & Cuboid box by order , SetBox , in tleap . The second one is that establish a Cubic box , 200*200*200 , by SetBox in tleap ,but I found the monomers don't filled the space in this periodic box ,and in MD process the supercell is disintegrated.
Above of all , I want to inqurie that how to establish a reasonable Triclinic box.
Index : 1. parameters of crystal in UnitCell
a=10.906 b= 3.991 c= 14.030 alpha=90 Belta= 110.82 gamma=90
2. Leap.in
source leaprc.gaff
mods = loadamberparams Mono.frcmod
MOL = loadmol2 Mono.mol2
check MOL
supercell = loadpdb 231.pdb
set supercell box { 200.0 200.0 200.0 }
saveamberparm supercell 231.prmtop 231.inpcrd
quit
3. min.in
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 1,
igb = 0,
ntr = 0,
cut = 20,
/
Yours Sincerely
2011-6-5
2011-06-05
hanlu0366
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Received on Sun Jun 05 2011 - 06:30:03 PDT
