AMBER Archive (2009)

Subject: RE: [AMBER] implicit solvent simulation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 06 2009 - 01:32:24 CDT

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

/\
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|\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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