Dear amber users
I am calculating binding free energy for my system (protein-ligand complex)
using amber. For this purpose, I used TUTORIAL A3: MM-PBSA
<
http://ambermd.org/tutorials/advanced/tutorial3/index.htm>. I prepared my
*.in files according to this tutorial. Based on section 1 in this tutorial,
I prepared 4 inpcrd and 4 prmtop files as follows (I used antechamber to
prepare inpcrd and prmtop for ligand):
1) protein.prmtop protein.inpcrd
2) ligand.prmtop ligand.inpcrd
3) complex.prmtop complex.inpcrd
4) complex_solvated.prmtop complex_solvated.inpcrd
Before I start MD simulation, I obtained pdb file related to solvated
complex using savepdb command. When I see this file by VMD, all things were
ok (please note the figure in the following link: (
https://www.dropbox.com/s/qwfedmbeug1infg/a.png?dl=0). Then I did MD
simulation of the solvated complex as follows:
----------------------------------------------------------------
minimise complex_solvated
&cntrl
imin=1,maxcyc=2000,ncyc=2000,
cut=10.0,ntb=1,
ntc=2,ntf=2,
ntpr=100,
ntr=1, restraintmask=':1-98',
restraint_wt=2.0
/
----------------------------------------------------------------
After minimization, all things were ok.
----------------------------------------------------------------
heat complex_solvated
&cntrl
imin=0,irest=0,ntx=1,
nstlim=100000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=310.0,
ntr=1, restraintmask=':1-98',
restraint_wt=2.0,
/
----------------------------------------------------------------
After heating, when I saw heat.mdcrd file using VMD, unfortunately, I
encountered with unusual structure (please note the figure in the following
link: (https://www.dropbox.com/s/tlsmhoaflpftzgc/b.png?dl=0).
What is the reason of this issue? I don’t use nmropt=1 in the heat.in file.
Is this important?
I am beginner in amber, please help me to resolve this problem.
Any help will highly appreciated.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 15 2015 - 01:00:02 PST
