3DRISM for complexes

This short tutorial will show you, how to set up a calculation for 3DRISM using AmberTools for several molecules/residues at one time.

The method is taken from the tutorial http://ambermd.org/tutorials/basic/tutorial4b/ , which has a different topic but nevertheless shows the necessary steps in detail.

How to do this

The most straight forward way is to create a pdb file with your desired complex, make sure every molecule has a different residue name. For each residue you copy the file and delete all other atoms. It is now possible to create your force field (ff) file for every residue separately. When using tleap, you add the line

saveoff MOL paracetamol.lib

'MOL' is the residue name, it should be used also in the pdb. 'paracetamol.lib' is the library file which says tleap, which ff to use for this residue. The name doesn't matter, but make sure it ends on 'lib'.

After doing this with all your residues, you can reload them with

loadoff MOL paracetamol.lib

Now you can assign the ff to your complex:

complex = loadpdb paracetamol_ch4.pdb
saveamberparm complex paracetamol_ch4.prmtop paracetamol_ch4.inpcrd

This commands load the pdb file and assign it to the internal variable complex. The informations for the ff of the residues takes it from the lib files. Please, take a look on the example below.

It is necessary, that all atoms in the complex and the residue files have the same name and position! That's why the method of extracting the residues out of the complex pdb is save. You can use different ff or different charging methods for the residues .

Example Paracetamol + Methan

Imagine you want to get the solvation free energy for a Paracetamol + Methan complex. It doesn't matter if this makes physically sense or not, but assigning the ff with antechamber is not directly possible. Antechamber tries to connect all atoms and therefore fails with a Paracetamol + Methan complex due to the large distances. This can be circumvented.

Download the and have a look on it. The residue is named MOL. You can open for example Maestro and add one Methan molecule and save this new complex as . Do not forget to delete all 'connections' assigned by Maestro in the pdb file, for antechamber cannot handle them.

You will see, the Methan got the residue name UNK. Now copy 'paracetamol_ch4.pdb' to '' and delete the MOL residue. Now you can run the following commands (they are saved in):

antechamber -i paracetamol.pdb -fi pdb -o paracetamol.mol2 -fo mol2 -c rc -cf paracetamol.charge -s 2
rm A*
antechamber -i ch4.pdb -fi pdb -o ch4.mol2 -fo mol2 -c cd
rm A*

parmchk -i paracetamol.mol2 -f mol2 -o paracetamol.frcmod
parmchk -i ch4.mol2 -f mol2 -o ch4.frcmod

#using tleap --> tleap.inp
echo "
source leaprc.gaff

MOL=loadmol2 paracetamol.mol2
loadamberparams paracetamol.frcmod

UNK=loadmol2 ch4.mol2
loadamberparams ch4.frcmod

saveoff MOL paracetamol.lib
saveamberparm MOL paracetamol.prmtop paracetamol.inpcrd

saveoff UNK ch4.lib
saveamberparm UNK ch4.prmtop ch4.inpcrd

loadoff paracetamol.lib
loadoff ch4.lib

complex = loadpdb paracetamol_ch4.pdb

saveamberparm complex paracetamol_ch4.prmtop paracetamol_ch4.inpcrd
savepdb complex paracetamol_ch4_out.pdb
" > tleap.inp

tleap -f tleap.inp

Paracetamol gets its partial charges out of the file 'paracetamol.charge'. Methan gets no charge at all. Now you are able to run 3DRISM with 'paracetamol_ch4_out.pdb' and 'paracetamol_ch4.prmtop'.