Sergey,
it's not clear to me, how you intend to mix parameters:
When you load the parameters for CpHMD via source leaprc.constph in
tleap, then you load the parameters for ff99SB (cf. Amber21 manual, p.
536). Although this includes the charge set for the TYR anion, you also
load ff99SB parameters for the other standard residues.
Thus, the protocol you suggested could work, if you intend to use the
forcefield implemented in CpHMD.
For parm14SB, you could utilize the charge set from the CpHMD setup and
generate an explicit new tyrosine-anion residue for parm14SB (it uses
the same charge model). For this, the standard TYR residue definition
may serve as template, but the atom type of the deprotonated oxygen may
have to be adapted.
Maybe that helps.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 29.03.2022 um 07:54 schrieb Пушкарев Сергей:
> 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 Tue Mar 29 2022 - 05:30:03 PDT
