Dear AMBER experts,
I have amber14 and AmberTools15 on my computer.
In preparing protein for MD simulations I use TLEAP procedure.
There are parameters in ff14SB force field for different forms of HIS: HID, HIE, HIP,
so TLEAP recognize and well differentiate them .
Unfortunately, I faced the problem with other ionized protein residues
like protonated neutral ASP and GLU side residues, or deprotonated
side residue of anionic SER gamma O atom.
It seems that the corresponding parameters for ionized side residues
are absent in the ff14BB force field, so TLEAP reports about fatal error.
I would appreciate if somebody can advise me how to work the problem around.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Thu Mar 10 2016 - 03:00:03 PST
