Dear Amber,
After reading a couple papers, mailing list and user manuals, we are not
100% sure if the following choice for protein-ligand (small molecule)
mmGBSA is justifiable.
igb
<*Preferable* bondi radii> (also doable)
Protein Force Field
Ligand Force Field
1
*mbondi in mmGBSA*
ff12SB
GAFF
2
*mbondi2 in mmGBSA* (bondi)
ff12SB
GAFF
5
*mbondi2 in mmGBSA* (bondi)
ff12SB
GAFF
7
*mbondi2 in mmGBSA *(bondi will cause instability in native peptide REMD)
ff12SB
GAFF
8
*mbondi2 in mmGBSA** (*mbondi3 in MD/REMD)
ff12SB
GAFF
In the previous mailing list, Hai and Jason mentioned that we should set
mbondi2 for igb=8 in protein-small molecule mmGBSA so this part is answered
already. However, in the paper of Hai et al. and Dill et al., they
mentioned that mbondi2 might be the better choice for igb=7 for
protein/peptide only simulation. Would you consider it would be the same
in protein-small molecule mmGBSA?
The other question is: Amber12 and AmberTools13 manuals clearly states
that we should use ff12SB for igb=7&8 but didn't recommend force field on
igb=1,2,5. Would you recommend to run igb=1,2,5 on ff12SB? Or ff99SB,
which igb=1,2,5 is frequently test on? Thank you.
Cheers,
Henry
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Received on Mon Jun 03 2013 - 10:00:03 PDT
