Hello amber users,
I am simulating a complex of two proteins and two ligands. After two
nanoseconds of simulations when I see the re-imaged trajectories on vmd, I
found that the water molecules moved away from solute and there seems no
box. This was the script that I used to make prmtop and inpcrd files. Could
you please tell me if there was a mistake. I am using amber10.
*tleap-1.in*
source leaprc.ff99SB
source leaprc.gaff
BI1 = loadmol2 BI-1001-1-new.mol2
BI2 = loadmol2 BI-1001-2-new.mol2
loadamberparams BI-1001-1-new.frcmod
loadamberparams BI-1001-2-new.frcmod
check BI1
check BI2
saveoff BI1 BI-1001-1-new.lib
saveoff BI2 BI-1001-2-new.lib
quit
*tleap-2.in
s*ource leaprc.ff99SB
source leaprc.gaff
loadamberparams BI-1001-1-new.frcmod
loadamberparams BI-1001-2-new.frcmod
set default PBRadii mbondi2
loadoff BI-1001-1-new.lib
loadoff BI-1001-2-new.lib
complex=loadpdb indimer_complex.pdb
receptor=loadpdb indimer_receptor.pdb
BI1=loadmol2 BI-1001-1-new.mol2
BI2=loadmol2 BI-1001-2-new.mol2
saveamberparm complex complex.prmtop complex.inpcrd
saveamberparm receptor receptor.prmtop receptor.inpcrd
saveamberparm BI1 BI1.prmtop BI1.inpcrd
saveamberparm BI2 BI2.prmtop BI2.inpcrd
solvatebox complex TIP3PBOX 10.0
charge complex
addions complex Na+ 0
charge complex
addions complex Cl- 0
saveamberparm complex solvated_complex.prmtop solvated_complex.inpcrd
savepdb complex solvated_complex.pdb
quit
Regards,
kamlesh
*
*
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Received on Wed May 23 2012 - 02:30:05 PDT
