The problem of annihilating the solute in the aqueous

From: Aurum Bai (javacfish_at_yahoo.com.cn)
Date: Mon Feb 22 2010 - 00:47:45 CST

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Dear all,

I do the "methane annihilating the solute in the aqueous" by FEP method.
When I copy new pdb's file to fep's file, I modify the B column of all fep's file to "-1" as below:

ATOM 1 CB METH 1 -0.987 -0.322 -25.473 1.00 -1.00 METH
ATOM 2 HB1 METH 1 0.035 0.102 -25.623 1.00 -1.00 METH
ATOM 3 HB2 METH 1 -0.997 -1.418 -25.274 1.00 -1.00 METH
ATOM 4 HB3 METH 1 -1.633 -0.089 -26.341 1.00 -1.00 METH
ATOM 5 HB4 METH 1 -1.446 0.190 -24.607 1.00 -1.00 METH
..................................................................

Then I run "alchemify setup.psf my.psf setup.fep" in vmd terminator, the err came:

"FEPfile : 5 atoms found, 5 initial, 0 final.
Either no atoms appearing, or no atoms disappearing.
PSF file requires no modification"

Must it have "-1"(vanish) and "1"(appear) at the same time?

How do I design this experiment to finish the methane shrinking in water and growing in gas?

Thanks very much~!

javacfish

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