AMBER Archive (2009)

Subject: Re: [AMBER] implicit solvent simulation

From: Manish Kumar (kumarmanish.amb_at_gmail.com)
Date: Thu Aug 06 2009 - 01:53:54 CDT

Thanks For the reply,

"Note I cannot comment on the appropriateness of your parameters for the non
standard ligand."
My ligand parameter does not has the new atom type. Is it still matter of
concern while using GB with my ligand. I am not sure how the GB radii are
assigned to the atoms?

And 1-215 is all residues of my system including ligand.

I am avoiding 2fs time step just because to minimize adverse affect of no
friction from solvent.

Sincerely,
Manish

On Thu, Aug 6, 2009 at 2:32 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Manish,
>
> > tleap -s -f leaprc.ff99SB
> > source leaprc.gaff
> > loadAmberParams LIG.frcmod
> > loadAmberPrep LIG_amber.prepc
> > set default PBradii mbondi2
> > com = loadpdb PROT_lig.pdb
> > check com
> > saveamberparm com cplx_wt_impli.prmtop cplx_wt_impli.inpcrd
>
> This looks good to me, you are using mbondi2 which is recommended for
> igb=5.
> Note I cannot comment on the appropriateness of your parameters for the non
> standard ligand.
>
>
> > Minimization script is:
> >
> > &cntrl
> > imin=1,maxcyc=2000,ncyc=1000,
> > cut=999.0,
> > igb=5,ntb=0,
> > ntc=2,ntf=2,
> > ntpr=100,
> > ntr=1, restraintmask=':1-215',
> > restraint_wt=50.0
>
> Looks okay. 50 kcal/mol is a little high but probably okay for
> minimization.
> What is the basis for you restraining residues 1 to 215? how much of your
> system does this represent? This is an implicit solvent run so you probably
> don't need to worry too much about restraints here if your initial
> structure
> is good. Perhaps you might want to minimize the ligand and protein in 2
> steps if you built this yourself but if it is from a reasonable pdb you
> probably can be more aggressive.
>
> > Heating Script is:
> >
> > &cntrl
> > imin=0,irest=0,ntx=1,
> > nstlim=100000,dt=0.001,
> > ntc=2,ntf=2,
> > cut=999.0,
> > igb=5,ntb=0,
> > ntpr=1000, ntwx=0,
> > ntt=3, gamma_ln=2.0,
> > tempi=0.0, temp0=300.0,
> > ntr=1, restraintmask=':1-215',
> > restraint_wt=5.0,
> > nmropt=1
> > /
> > &wt TYPE='TEMP0', istep1=0, istep2=100000,
> > value1=0.1, value2=300.0, /
> > &wt TYPE='END' /
>
> This looks okay. Note you may want to set ntwx>0 so you get a trajectory
> output that you can look at to make sure things look okay. You might also
> want to consider a 2fs timestep. With shake you should be okay with this
> and
> then you would get double the sampling. As for the restraints think about
> if
> you really need them. Residues 1 to 215 seems like a good chunk of your
> system for an implicit solvent simulation. Do you really need the
> restraints?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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