Hi,
> 1) I have been completely unable to do this process with AmberTools12
> "tleap" using the "delete" command (actually I cannot find it in the
> manual) BUT using "remove" I can delete the solute from the solvent box
> using the sequence:
um, yes, I guess I meant remove instead of delete...
> solvatebox ANQ TIP4PEWBOX 10.0
> setbox ANQ vdw
this should do no harm, but solvatebox automatically performs a setbox on
your system, so the setbox line could be left out.
> 2) Then I face a new problem. The cartesian coordinates of the water
> molecules in the V0 and V1 states are exactly the same, BUT, the atom
> numbers and the the residue numbers in the solvent box have been shifted
> after the solute removal:
that is fine, when you set scmask=':1', then the first non-softcore water
atom in V0 will be the same one as in your V1 water-only box. The actual
atom numbers are not used for this purpose, sander knows which atoms to
skip and which to match when the mask is set correctly.
> And then, according to the amber12 manual for the Thermodynamic
> Integration I read:
>
> "The input (mdin) and starting coordinate files must be the same for the
> two groups. Furthermore, the two prmtop files must have the same number
> number of atoms, in the same order (since one common set of coordinates
> will be used for both.)..." [pg. 114]
this may refer to the case of doing TI when ifsc=0, i.e. no softcore atoms
are used.
> ... so... what can I do?
go ahead and run your simulation, it should work the way you describe :-)
> 3) Thomas, could you please recommend me any reference about the 1- and 2-
> step transformations "in explicit solvent" and "in gas phase"? I am very
> curious about the practical and theoretical aspects of the transformation
> when in some cases you need the "in vacuo" step to close the cycle and in
> others no (regarding the charge removal)
Try this:
Title: Soft-Core Potentials in Thermodynamic Integration: Comparing One-
and Two-Step Transformations
Author(s): Steinbrecher, Thomas; Joung, InSuk; Case, David A.
Source: JOURNAL OF COMPUTATIONAL CHEMISTRY Volume: 32 Issue: 15
Pages: 3253-3263 DOI: 10.1002/jcc.21909 Published: NOV 30 2011
the point of being able to leave out the vacuum steps completely is merely
a matter of defining your zero-point. It perfectly works for the single
step transformation case because there all intramolecular interaction in
the solute stay intact. For the two step case, 1-4-electrostatics change
in the solvated charge removal steps and therefore need to be calculated
in vacuo as well.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Mar 20 2013 - 03:00:05 PDT
