Hi Surgey,
We had develop charges and refitted chi1/chi2 for Tyrosine anion (TYD). I
have attached the .lib and .frcmod files here. You can use TIP3P or OPC
with ff14SB.
Here is a leap.in file
source leaprc.protein.ff14SB
source leaprc.water.opc
loadoff ./TYDllib
loadAmberParams ./TYD.frcmod
x = sequence {ACE TYD NME}
check x
savepdb x TYD.14SB.nowat.new.pdb
solvateoct x OPCBOX 14
saveamberparm x TYD.14SB.opc.new.parm7 TYD.14SB.opc.new.rst7
quit
For security reasons I cannot upload .lib files so I upload it as
.lib.remove. So just change the name from TYD.lib.remove to TYD.lib.
Let me know if you have any questions.
Kellon A. A. Belfon, PhD
Computational Chemist
Phone: (347) 546-4237 <(347)+546+4237> Email: kellonbelfon.gmail.com
<kellonbelfon.gmail.com>
On Tue, Mar 29, 2022 at 8:01 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Tue Mar 29 2022 - 10:00:02 PDT
