Hello:
Coming to AMBER ff12SB with a protein extensively equilibrated with
CHARMM 27 ff, I wonder whether it is worth trying to save the initial
position of H-atoms. Of course, I tried manually to adapt the layout
to AMBER.
I could not find much help from LEaP (ambertools 12) manual or the archive.
On applying code
protonate -k -d $AMBERHOME/dat/PROTON.INFO -i input.pdb -o output.pdb
-l protonate.log
it is only with ILE CH2-CH3 that the three methyl hydrogens are said
"mysterious" and where removed in the output pdb. Of course all
H-atoms of the organic small ligand were removed (I did not try to
give the info on atom names from the used antechamber, should that be
possible at all).
That would not be a bad prospect if the missing H-atoms (BUT ONLY
THEM) are added during LEaP work out. Is it a command to get that with
LEaP? Are these efforts worth while or is it safer to let LEaP
replacing all H-atoms?.
Thanks a lot for your advice
francesco pietra
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Received on Sat May 26 2012 - 07:30:02 PDT
