Hello, Amber users!
I want to simulate a protein with a tyrosine anion residue. Just do a plain
MD, not a CpHMD run. I could find in the previous mailing list discussions
that I could do something like this:
1) make the .prmtop and .inpcrd files using tleap.
2) In ParmEd do "changeProtState <tyrosine atoms> 1" and write a new
.prmtop file which will have zeroed LJ and charge parameters for the HH
atom.
3) just do a normal MD with the modified .prmtop file. No special flags for
CpHMD are needed.
Will this protocol work for me?
Could someone provide me with the reference for the modified charges of Tyr
to cite? Also I don't know what protein forcefield I must use to be
consistent with Tyr anion charges. Will ff14SB with tip3p work?
Best regards,
Sergey Pushkarev
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Received on Mon Mar 28 2022 - 23:00:02 PDT
