AMBER Archive (2008)

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

From: yongleli (yongleli_at_itcc.nju.edu.cn)
Date: Wed Jul 02 2008 - 13:19:03 CDT

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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