Dear Enrico,
> For the test of the simulation with PBC I would like to create a simple
> system containing the mix of TIP3P water with ethanol and placing some
> glucose molecules inside. Previously I performed simulations of proteins
> solvated in a water box but never the pure liquid. Could you please suggest
> to me what would be the right order of tleap commands to create such a
> multi-component solvent system ?
You could use a feature of the LEaP program:
LEaP can add missing atoms in a PDB file based on the atoms found in
the FF libs...
see
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#Bpol2
Let's say you have 3 FF libs for Water, Ethanol & D-Glc
- Water FF lib./mol2 file contains the OW/HW atom names and WAT residue name
- EtOH FF lib./mol2 file contains the OH/HO atom names (among others)
and ETO residue name
- D-Glc FF lib./mol2 file contains the O1/O2 atom names (among others)
and GLC residue name
You solvate water by itself, generate a box of let's say 1000 water
molecules and save to the PDB file format.
You keep only the oxygen atoms:
egrep "OW|TER" Box-water.pdb > Box-water-Only-OW.pdb
You replace 10 'OW' atoms in Box-water-Only-OW.pdb by 'OH' using 'sed/awk':
'OW WAT' -> 'OH ETO' 10 times
You replace 140 'OW' atoms in Box-water-Only-OW.pdb by 'O1' using the
same approach:
'OW WAT' -> 'O1 GLC' 140 times
You load the 3 FF libs and _then_ Box-water-Only-OW.pdb; LEaP should
add the missing atoms in the PDB file according to the FF lib
atom/residue names. You end up with a box of 3 solvents that has to be
equilibrated (the purcentages are in number of molecules)...
Best Francois
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Received on Fri Oct 18 2024 - 04:00:02 PDT
