Just to second Anselm’s reply: If you are fine with the FF99SB forcefield, you can follow the tleap -> parmed -> pmemd-for-normal-MD procedure you mentioned. In the parmed step you specify the protonation state of the Tyr, and if you don’t give pmemd a cpin file, the Tyr will retain the protonation state you assigned (no titration occurs).
Best,
Matthew
> On Mar 29, 2022, at 8:00 AM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> 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 - 06:00:02 PDT
