AMBER Archive (2008)

Subject: Re: AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Wed Jul 02 2008 - 14:08:40 CDT

Hi yongleli,

you cannot (and need not) run a TI calculation in which your complete
system disappears, amber is not equipped to handle an empty input file.

You can check the ifsc=2 option gives you a useful result, which would
involve running a calculation only on the benzene molecule in vacuum
and dVdl calculated compared to a hypothetical empty system in which all
energies are zero.

However this should not be necessary. Softcore TI automatically excludes
all internal interactions (bonds, angles, vdw) in the disappearing benzene
from dG2 as well as dG1, therefore the free energy change for moving from
a benzene to 'nothing' should be zero.

Let me know if this gives you an acceptable result,

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Thu, 3 Jul 2008, yongleli wrote:

> Dear Amber users,
>
> I am trying to calculate the solvation free energy of benzene using newly developed soft-core potential, just as the Amber tutorial A9. The thermodynamic cycle I choose is the one in Fig 2 of Chem. Rev. 2000, 100(11), 4187:
> dG1
> gas A -------> dummy
> | |
> dG3 | | dG4
> | |
> solution A--------> dummy
> dG2
>
> dGsol(A)=dG1-dG2
>
> When I calculate dG2, I used two set of parmtop and rst files. One contains a benzene molecule and water box, but the other contains only water box. The benzene is scaled to dummy along lambda changing from 0 to 1. And the calculation worked.
>
> But when I calculate dG1, I prepared one set of input files containing only a benzene molecule, and the other containing nothing with similar consideration. But when I did dis, I got a blank rst file, and cannot perform the calculation with the error notice:
>
> forrtl: severe (24): end-of-file during read, unit 9, file /home/yongle/dd/null_v.rst
>
> Then I changed the rst file with a blank line, a number 0 denotes there is no atom, and box information
> the same as the last line in the rst file containing benzene molecule. Then the error output is:
>
> ERROR: Flag "SOLVENT_POINTERS" not found in PARM file
>
> Now I have no idea of other solution. Who can tell me what I must do for calculate dG1?
> Here are the two input files I used of the first minimization step of calculation of dG1.
>
> minimization
> &cntrl
> imin = 1, ntx = 1,
> maxcyc=500,
> ntpr = 100,
> igb =0,
> ntmin = 2,
> ntb = 0, cut = 999.0,
> icfe=1, clambda = 0.50000,
> jfastw=4, noshakemask=':BNZ_at_C1,C2,C3,C4,C5,C6,H1,H2,H3,H4,H5,H6',
> ifsc=1,
> scmask=':BNZ_at_C1,C2,C3,C4,C5,C6,H1,H2,H3,H4,H5,H6',
> crgmask=':BNZ_at_C1,C2,C3,C4,C5,C6,H1,H2,H3,H4,H5,H6'
> &end
>
> minimization
> &cntrl
> imin = 1, ntx = 1,
> maxcyc=500,
> ntpr = 100,
> igb =0,
> ntmin = 2,
> ntb = 0, cut = 999.0,
> icfe=1, clambda = 0.50000,
> jfastw=4, noshakemask='',
> ifsc=1,
> scmask='',
> crgmask=''
> &end
>
>
>
>
> yongleli
> 2008-07-03
>
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