GROMACS version: 2021
GROMACS modification: No
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I have two conserved water molecules, which should be considered as ligands interacting with the protein. The [ molecules ] section in the topology file is like this. The first SOL group has 2 molecules, which represents the 2 conserved water; the second SOL group is the solvent water. But these two SOL groups essentially share the same water topology (i.e. tip3p.itp).
[ molecules ]
; Compound #mols
But I think I also need to add a new [ moleculetype ] specifically for the two conserved water, and use the same POSRES position restraints as protein
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
to constrain the 2 conserved water, so that define = -DPOSRES will constrain not only the protein but also the 2 conserved water. Can I ask what I need to modify to this new [ moleculetype ]? Is there a explanation for the default tip3p.itp (e.g. #ifndef FLEXIBLE, [ settles ]) ?
If you want to position restrain the 2 conserved water molecule you can copy the water topology in your working dir, change the name of the itp file and change the molecular name in the file. Update the [molecules] directive in topol.top and include the new water topology in the correct order in the topol.top together with a new POSRES definition (with a different name from the water one). Then add the new POSRES name in mdp file.
But I wonder if you really need this, since (I guess) you will release the restrain in data production and the water molecules usually exchange with another water molecule.
Hi @alevilla, thank you very much. I think I am following your instructions:
I save the default tip3p.itp as tip3p1.itp and put into my working directory, replace all the SOL strings with FIX. But I am not sure how to deal with the [ settles ] and [ exclusions ] sections. Based on this thread, I replace the [ settles ] and [ exclusions ] sections with [ constraints ], is that correct? But that thread is for “flat-bottom restraint”, what if I want to use the normal “position restraint”?
[ moleculetype ]
; molname nrexcl
[ atoms ]
; id at type res nr res name at name cg nr charge mass
1 OW 1 FIX OW 1 -0.834 16.00000
2 HW 1 FIX HW1 1 0.417 1.00800
3 HW 1 FIX HW2 1 0.417 1.00800
;;[ settles ]
; OW funct doh dhh
;;1 1 0.09572 0.15139
;;[ exclusions ]
;;1 2 3
;;2 1 3
;;3 1 2
[ constraints ]
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139
[ bonds ]
; i j funct length force_constant
1 2 1 0.09572 502416.0 0.09572 502416.0
1 3 1 0.09572 502416.0 0.09572 502416.0
[ angles ]
; i j k funct angle force_constant
2 1 3 1 104.52 628.02 104.52 628.02
Yes, I have also updated the topology file to include the new water molecule. But I use the same POSRES for the conserved water as protein.
Sorry I do not think so. If the [ settles ] and [ exclusions ] sections are kept in the conserved water, this error occurs:
The [molecules] section of your topology specifies more than one block of
a [moleculetype] with a [settles] block. Only one such is allowed. If you
are trying to partition your solvent into different *groups* (e.g. for
freezing, T-coupling, etc.) then you are using the wrong approach. Index
files specify groups. Otherwise, you may wish to change the least-used
block of molecules with SETTLE constraints into 3 normal constraints.
Thank you Justin, would it be possible if you can show me an example for the “three constraints” for “position restraint”? Is it the same for “position restraint” and “flat-bottom restraint” (earlier thread)?