I am working with a protein (human histone deacetylase, a metalloprotein,pdb 2v5w). I want to run some simulation studies in amber but I am unable to add hydrogen to this molecule. How should one estimate the charges on it for further simulation. I am using amber package
The Amber program will automatically protonate (add hydrogen atoms) the system.
However, you must be carefully in defining the right protonation state of the amino acid acid residues especially the Histidines (HID, HIP or HIE) during the protein preparation step. See Article A Novel Class of Schistosoma mansoni Histone Deacetylase 8 (...
and more there for the most common protocols and software used
Hashim Shah
I suspect you are getting the error when running "tleap" command and the reason could be that you don't have any information for your organic ligand...
if so, you should work first in generating the proper charges for your ligand... of course, you will need to add the hydrogen with avogadro or chemaxon (personally, I prefer chemaxon) and then use antechamber for generating the proper .mol2 file
antechamber -i ligand_h.mol2 -fi mol2 -o ligand.mol2 -fo mol2 -c bcc -s 2 -eq 2 -at gaff
Then, use parmcheck2 in order to generate missing parameters for your ligand...
parmchk2 -i ligand.mol2 -f mol2 -o ligand.frcmod
Lastly, run tleap program...
tleap -f tleap.in (see below the content you have to put in tleap.in file)
source leaprc.ff14SB
source leaprc.gaff
PROT = loadpdb protein.pdb
LIG = loadmol2 ligand.mol2
COM = combine {PROT LIG}
check LIG
loadamberparams ligand.frcmod
saveoff LIG ligand.lib
saveamberparm PROT protein.prmtop protein.inpcrd
saveamberparm LIG ligand.prmtop ligand.inpcrd
saveamberparm COM complex.prmtop complex.inpcrd
savepdb complex.pdb
quit
hope this helps!
Dear Hashim
You can use reduce command.
reduce xyz.pdb > xyz_h.pdb
but before going to run MD simulation check whether it has added hydrogen in the correct or not.
If you want some online server help use H++ server it will check protonation state and added hydrogen also but it is not good for ligand.
Second thing please mention the error in TLEAP as it always show some error or warnings. So it will be good for us to understand the problem.
Thank you all Mario E. Valdés-Tresanco especially you. The recommendations worked.
You can also use iCn3D with the menu "Analysis > Download PQR", e.g., https://structure.ncbi.nlm.nih.gov/icn3d/share.html?B1uygHNnip1e9KNv9
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