Dear Lenka,
The settings in the file you provided are appropriate for a Charmm
simulation. Will you be using Amber force fields? If so, I recommend using
input parameters similar to those in the Amber lipid force field tutorial:
http://ambermd.org/tutorials/advanced/tutorial16. For membrane protein
simulations, you may need a few adjustments. Does anyone know of a paper or
tutorial that would provide a better reference for that purpose?
Best,
Sally
Sally Pias
Associate Professor of Chemistry
Faculty Adjunct, Department of Biology
New Mexico Tech
On Wed, Nov 28, 2018 at 10:56 AM Stejskal, Lenka <
lenka.stejskal.15.ucl.ac.uk> wrote:
> Dear Amber users,
>
>
> I always perform minimisation using the ntb=1 and therefore with periodic
> boundary under constant volume.
>
>
> I am attempting to simulate membrane protein now. I have generated
> membrane using CHARMM GUI and this is the minimisation control file that
> was generated for me by the software:
>
>
> Minimization input file in explicit solvent
> &cntrl
> ! Minimization options
> imin=1, ! Turn on minimization
> maxcyc=5000, ! Maximum number of minimization cycles
> ncyc=2500, ! 100 steepest-descent steps, better for strained
> systems
>
> ! Potential energy function options
> cut=12.0, ! Nonbonded cutoff, in Angstroms
> fswitch=10.0, ! Force-based switching
>
> ! Control how often information is printed to the output file
> ntpr=100, ! Print energies every 100 steps
> ntxo=2, ! Write NetCDF format
>
> ! Restraint options
> ntr=1, ! Positional restraints for proteins, sugars, ligands,
> and lipid head groups
> nmropt=1, ! Dihedral restraints for sugars and lipids
>
> ! Set water atom/residue names for SETTLE recognition
> watnam='WAT', ! Water residues are named WAT
> owtnm='O', ! Water oxygens are named O
> /
>
> &ewald
> vdwmeth = 0,
> /
>
> &wt
> type='END'
> /
> Protein posres
> 10.0
> RES 1 227
> END
> Membrane posres
> 2.5
> FIND
> P * * POPC
> SEARCH
> RES 1 11740
> END
> END
>
> DISANG=step6.0_minimization.rest
> LISTIN=POUT
> LISTOUT=POUT
>
>
>
> The ntb is not set to 1. Can I proceed with this?
>
> Thank you
>
> L.
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Received on Wed Nov 28 2018 - 11:00:04 PST
