Thanks for your reply.
By asking "correctness" of the script, I mean to ask the consistency of the
different parameters with igb=5, which I assume, according to you is
correct.
I am not interested in polarizable force field as my customized ligand will
not have parameter for that.
I think slow heating at very first step of simulation makes sure that
structure will not go into abrupt structural changes and will go to the
equilibration relatively faster. However, putting position restrain on the
atoms will also make sure that that system is not adopting some undesirable
structural change. I think heating the molecule is the recommended practice
before equilibrating the system, especially in implicit solvent where there
is no solvent friction. And as far as I know, the "equilibration" and
"production" are the poorly defined terms in computational chemistry,
especially while working with the biomolecules, and therefore slow heating
perhaps helps overcoming uncertainty in definitions.
Manish
On Thu, Aug 6, 2009 at 1:00 AM, Ashish Runthala
<ashish.runthala.gmail.com>wrote:
> See the script is correct but check for the restraintmask format as it
> is different in different AMBER versions. And also check whether you
> need to use the polarized state or not by using ipol=1, and
> saveamberparmpol.
> See there are many runs like equilibration run and production run
> instead of directly going to heating run. Just watch out what you are
> attempting.
>
> On Thu, Aug 6, 2009 at 1:49 PM, Manish Kumar<kumarmanish.amb.gmail.com>
> wrote:
> > Dear Experts,
> >
> > I am doing implicit solvent simulation.
> >
> > My tleap commands were:
> >
> > 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
> >
> >
> > 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
> >
> > 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' /
> >
> > I will be very thankful if someone can look over these scripts and
> assure
> > me that these are correct.
> >
> > Manish
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Ashish Runthala,
> Faculty Division III,
> Lecturer, Biological Sciences,
> Birla Institute of Technology and Science,
> Pilani, Rajasthan- 333031
> INDIA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 20:37:30 PDT
