Greeting,
I want to run MD simulation of Ruthenium complex to determine the
counter-ion distribution around the complex. What I have done so far:
1) I generated frcmod for the complex and NH4 with the needed parameters
and charges that I calculated. Ru.frcmod, NH4.frcmod
2)using packmol I created a cubic box with the desired concentration of the
complex molecules and the ions (NH4+) in 95% of ethanol as solvent. Then
save the coordination as (all.pdb)
3) from the created all.pdb file, I extracted the complex and ions into
another pdb file (solu.pdb) and with tleap I created the mol2 file that
included all solute molecules and soul.prmtop and solu.inpcrd
** Now I want tleap to read the solvent box and this is the approach I want
to do**
1) from all.pdb generated by packmol I will extract the solvent
(ethanol+water) into other file (solv.pdb)
2) changing the water residue name from HOH to WAT, HETATOM to ATOM, TER
each molecule (this will require a lot of work)
3) then run tleap
>> tleap
>> source leaprc.gaff (to read ethanol)
>> source leaprc.water.tip3p (for the water)
>> solv = loadpdb solv.pdb
>> all=combine{solu.pdb solv.pdb}
>> addition all Cl- 0 (to neutralize the system)
>> savepdb all all_amber.pdb
>> saveamberparm all all.prmtop all.inpcrd
Is this the right approach to read the solvent parameters from AMBER
library files for solvent box generated by packmol?
Best,
Sanaa AlAbbad
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Received on Mon Sep 18 2017 - 15:30:02 PDT
