OK, I notice that I can run the same script with sander but not with
pmemd.cuda. Maybe because I am using the AMBER12 version.
Btw, I made a typo in my previous email. It should had been imin=1, maxcyc
= 1000, ncyc = 500.
On 22 September 2016 at 18:54, Thomas Evangelidis <tevang3.gmail.com> wrote:
> 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/
>
>
--
======================================================================
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/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 22 2016 - 16:30:02 PDT
