[19-III-2013]
Hi Thomas and Ignacio,
I have tried to create the input files for the boxes
V0 = [solvent+solute], and
V1 = [solvent]
according to the method proposed by Tom: creating system crd + top files, then using "delete system system.1" and saving again:
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:
**********************************************************
source leaprc.ff99SB
loadamberparams frcmod.tip4pew
loadoff solvents.lib
loadoff anq.lib
solvatebox ANQ TIP4PEWBOX 10.0
setbox ANQ vdw
check ANQ
set default PdbWriteCharges on
savePDB ANQ anqWAT.pdb
saveMol2 ANQ anqWAT.mol2 1
saveamberparm ANQ anqWAT.top anqWAT.crd
remove ANQ ANQ.1
savePDB ANQ anqBOX.pdb
saveMol2 ANQ anqBOX.mol2 1
saveamberparm ANQ anqBOX.top anqBOX.crd
quit
**********************************************************
Do they (delete remove) do exactly the same?
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:
New atom number = old atom number - number of atoms in the solute molecule
Number of residue = old residue number - 1.
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]
... so... what can I do?
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)
Actually I was thinking precisely in:
> You dont need to do this anymore. The tranformation keeps internal
> energies intact, so the dG for solute->nothing always equals 0.0.
>
> You do need to do the vacuum charge removal for the solute though. That
> can be avoided by switching to one-step transformations if you want to.
Sorry for being so persistent with this doubt.
I send attached the PDB files after solvent removal and the library of the organic molecule in case is of any help.
Thank you very much!!
Kepa K.
*******************************************************
________________________________
De: "steinbrt.rci.rutgers.edu" <steinbrt.rci.rutgers.edu>
Para: AMBER Mailing List <amber.ambermd.org>
Enviado: Martes 19 de marzo de 2013 11:07
Asunto: Re: [AMBER] Hydration Free Enery by TI
Hi,
> But this may be a problem when you are disappearing, say, one residue in a
> stretch of RNA, since then you will end up with two separate pieces of
> RNA.
but, if you are removing an RNA base in the middle of a strand, you do
want to end up with two separate pieces of DNA, dont you? Removing one
base and subsequently closing the gap would be two big changes to simulate
at once and I am not sure if a typical TI calculation would converge well
on this. You could do it by deleting residue n in v1 and adding a (very
long) bond between residues n-1 and n+1 at the appropriate place in leap.
This transformation sounds like horribly difficult sampling to me, though.
> So, I am wondering, is it possible to do in the VDW step what one usually
> does for the charge, i.e,
>
> crgmask_v0=:10
> scmask_v0=''
> crgmask_v1=:10
> scmask_v1=:10
>
> while using the same prm and rst file for both V0 and V1? (in V0 you have
> a
> residue 10 without charge but with VDW, while in V1 you have residue 10
> without charge and without VDW).
No, you cant set things up this way. The syntax you describe would make
sense for disappearing residues, but that is not how the current code
works.
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 Tue Mar 19 2013 - 13:00:02 PDT
