Oh since you are running the MD on a protein with TYR, you can probably
just use the charges for TYD and use TYR chi1/chi2 parameters.
so leap.in
source leaprc.protein.ff14SB
source leaprc.water.opc
loadoff ./TYD.lib
x = loadpdb xx.pdb
So in that way you do not overwrite the TYR chi1/chi2. I will need to add a
new atom type to allow mixing.
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 12:40 PM Kellon Belfon <kellonbelfon.gmail.com>
wrote:
> 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
