Dear AMBER list members,
I need some trouble shooting to run minimization and MD of a protein-ligand
complex without using GB radii. I want to do that by including some
explicit waters in the binding cavity (which is the only place of interest)
and preventing them from defusing by imposing restraints. So 1st question:
is it necessary to use an external dielectric constant of 1 (extdiel=1)?
Here is how I created my prmtop and inpcrd files:
source leaprc.protein.ff14SBonlysc
source leaprc.water.tip3p
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams frcmod.ions234lm_126_tip3p
source leaprc.gaff
loadAmberParams frcmod.ligand
# choose the appropriate set of GB radii (igb=1->mbondi; igb=2->mbondi2;
igb=5->mbondi2; igb=7->bondi; igb=8->mbondi3)
set default pbradii
protein = loadpdb receptor.pdb
LIG = loadMol2 ligand.antechamber.mol2
complex = combine { protein LIG }
# add a solvent sphere centered at the ligand COM and with radius 8 + 12.0
Ang.
solvateCap complex TIP3PBOX complex.LIG 20 1.0
savePDB complex tmp_complex.pdb
complex2 = loadpdb tmp_complex.pdb
savePDB complex2 protein-ligand.pdb
saveAmberParm LIG ligand.prmtop ligand.inpcrd
saveAmberParm complex2 complex.prmtop complex.inpcrd
quit
My minimization script looks like this:
# minimization
&cntrl
imin = 1000,
maxcyc = 500,
ncyc = 0,
ntb = 0,
ntp = 0,
igb = 0,
extdiel = 1,
cut = 999,
ntpr = 10,
ntr=1, ntrx=1, restraint_wt=100,
restraintmask="! ( (:LIG <:8) | :LIG )"
/
But pmemd.cuda gave the following error:
| ERROR: nfft1 must be in the range of 6 to 512!
| ERROR: nfft2 must be in the range of 6 to 512!
| ERROR: nfft3 must be in the range of 6 to 512!
| ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: b must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
Any ideas how to solve this?
thanks in advance
Thomas
--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Sep 22 2016 - 10:00:02 PDT
