Hi Alexey,
The Zn ion unbinds in all the force fields, so it is not extremely important for stability but probably plays some role (and happened to be bound in this longer unstructured region). I didn't notice anything special about the divalent ion behavior in OPC3-pol, it seemed to be about as bad in keeping them in place as the others. One should use constraints with divalent ions if they should stay in place.
Cheers,
Piia
--
Piia Bartoš, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 | piia.bartos.uef.fi<mailto:
piia.bartos.uef.fi>
________________________________
From: alexey <alexey.cs.vt.edu>
Sent: Monday, May 22, 2023 23:14
To: Piia Bartos <piia.bartos.uef.fi>
Cc: AMBER Mailing List <amber.ambermd.org>; Yeyue Xiong <xiongyy.vt.edu>
Subject: Re: [AMBER] OPC3-pol
Hi Piia,
chiming in...
Skimmed through the paper, very interesting and useful!
Somehow I am not surprised that OPC3-pol may be destabilizing extended loop regions, I have a suspicion that the model shifts the compact-extended balance just a ted away from where it should be. We have seen it produce a nearly random coil ensemble for an IDP, where a bit more compact structure was expected. It is interesting that AMOEBA model seems to show a similar trend, though to a lesser extent.
I saw a Zn ion in one of the pictures near the loop, do you think it is stabilizing the structure? We have not checked how divalent ions behave in the presence of OPC3-pol.
regards, Alexey
On 2023-05-22 07:04, Piia Bartos wrote:
Hi Yeyue,
Yes, I managed to run the OPC3-pol simulations by making a slightly larger box (12Å buffer instead of 10Å) and taking the box dimensions from an equilibrated OPC box and inputting them manually on tleap. I also doubled the equilibration steps just to be on the safe side, but this might not be necessary. The simulations ran fine, but they displayed some issues with structural integrity especially if the protein had longer loop regions. More details in the preprint: https://chemrxiv.org/engage/chemrxiv/article-details/6454e4fb1ca6101a45d1a67d
Hopefully it is easier now for other users as well, I need to try this new method for the next system. :)
Cheers,
Piia
--
Piia Bartoš, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 | piia.bartos.uef.fi
________________________________
From: Yeyue Xiong <xiongyy.vt.edu>
Sent: Saturday, May 20, 2023 03:36
To: Piia Bartos <piia.bartos.uef.fi>; AMBER Mailing List <amber.ambermd.org>
Cc: alexey <alexey.cs.vt.edu>
Subject: Re: [AMBER] OPC3-pol
Hello Piia,
Just want to follow up on this -- were you able to run your simulations with OPC3-pol after the last email?
We added a pre-equilibrated waterbox for OPC3-pol -- `OPC3POLBOX` to AMBER 23, now you can do `solvatebox molc OPC3POLBOX 10.0` in tLEAP instead of `O3P` as in the previous version. More details can be found in Amber23 manual.
Best regards,
Yeyue
On Tue, Nov 29, 2022 at 9:50 AM Yeyue Xiong <xiongyy.vt.edu<mailto:xiongyy.vt.edu>> wrote:
Hi Piia,
Could you try replacing this line `solvatebox molc OPC3BOX 10.0` with -
`solvatebox molc O3P 10.0` ? (this might need a longer equilibration stage since it's not a pre-equilibrated water box like `OPC3BOX` etc.)
It looks like tleap solvated the system with opc3(OP3) while still thinking the WAT is opc3-pol (O3P).
Best,
Yeyue
On Sat, Nov 26, 2022 at 12:06 AM Piia Bartos via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
Hi,
I can share the cpptraj as well. Like the other scripts, this works fine with the other water models, so my assumption is that there is some bug...
Here is the script:
parm structure_HMR.prmtop
reference structure.inpcrd [ref]
trajin prod1.nc<
http://prod1.nc/> 1 last 1
#strip :WAT outprefix stripped
center .CA mass origin
image origin center familiar
rms ref [ref] mass out rmsd.out @CA fit
trajout stripped.xtc
Cheers,
Piia
--
Piia Bartoš, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 |
piia.bartos.uef.fi<mailto:
piia.bartos.uef.fi><mailto:
piia.bartos.uef.fi<mailto:
piia.bartos.uef.fi>>
________________________________
From: Saeed Izadi <izadi.vt.edu<mailto:izadi.vt.edu>>
Sent: Thursday, November 24, 2022 09:08
To: Piia Bartos <piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Cc: Carlos Simmerling <carlos.simmerling.gmail.com<mailto:carlos.simmerling.gmail.com>>
Subject: Re: [AMBER] OPC3-pol
I wonder if there is an issue in your post-processing and visualization of the trajectory than with the simulation itself. Did you process your trajectory in cpptraj (e.g. "autoimage" and "rms first") before visualization? If so, would you share your cpptraj scripts as well?
On Tue, Nov 22, 2022 at 11:58 PM Piia Bartos via AMBER <amber.ambermd.org<mailto:amber.ambermd.org><mailto:amber.ambermd.org<mailto:amber.ambermd.org>>> wrote:
Hi,
I am using AmberTools22, which was installed on our supercomputer last week along with Amber22 (no issues during installation and/or testing). So it should have all the necessary patches.
I just tested, the HMR is not the issue, similar behavior happens also without it at 2fs timestep.
Here is the tleap:
source leaprc.protein.ff19SB
source leaprc.RNA.OL3
WAT = O3P
source leaprc.water.opc3pol
loadAmberParams frcmod.opc3pol_HMR4fs
loadAmberParams frcmod.ionslm_126_opc
molc = loadPdb "input.pdb"
solvatebox molc OPC3BOX 10.0
addIonsRand molc Na+ 88
addIonsRand molc Cl- 92
saveAmberParm molc structure.prmtop structure.inpcrd
savePdb molc structure.pdb
quit
Cheers,
Piia
--
Piia Bartoš, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 | piia.bartos.uef.fi<mailto:
piia.bartos.uef.fi><mailto:
piia.bartos.uef.fi<mailto:
piia.bartos.uef.fi>><mailto:
piia.bartos.uef.fi<mailto:
piia.bartos.uef.fi><mailto:
piia.bartos.uef.fi<mailto:
piia.bartos.uef.fi>>>
From: Carlos Simmerling <carlos.simmerling.gmail.com<mailto:carlos.simmerling.gmail.com><mailto:carlos.simmerling.gmail.com<mailto:carlos.simmerling.gmail.com>>>
Sent: maanantai 21. marraskuuta 2022 18.13
To: Piia Bartos <piia.bartos.uef.fi<mailto:piia.bartos.uef.fi><mailto:piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org><mailto:amber.ambermd.org<mailto:amber.ambermd.org>>>
Subject: Re: [AMBER] OPC3-pol
can you share your leap input, and which version of AmberTools you are using? is it fully up to date with patches?
if you suspect HMR, did you try a run without HMR?
On Mon, Nov 21, 2022 at 6:21 AM Piia Bartos via AMBER <amber.ambermd.org<mailto:amber.ambermd.org><mailto:amber.ambermd.org<mailto:amber.ambermd.org>><mailto:amber.ambermd.org<mailto:amber.ambermd.org><mailto:amber.ambermd.org<mailto:amber.ambermd.org>>>> wrote:
Hi Amber people,
I tried to test the new OPC3-pol water model with my protein system.
It seems to be incompatible with some of my simulation parameter, as the simulations with the OPC3-pol water appear to be "frozen", where atoms remain almost still thorough the simulation (500 ns). The same production script works fine for OPC water model. Any ideas what I need to change? The issue might be with the Parmed, HMR and using 4fs timestep, but I think I built the system correctly...
Here is the production script:
# 500 ns production Langevin thermostat + Monte carlo barostat dynamics
&cntrl
imin=0,
irest=1, ntx=5,
ntpr=25000, ntwx=25000, ntwr=25000,
ntb=2, barostat=2, cut=10, iwrap=1,
nstlim=125000000, nscm=0, dt=0.004,
ntt=3, gamma_ln = 1, ig=-1, temp0=310, tempi=310,
ntp=1,
ntc=2, ntf=2,
ioutfm=1,
/
&ewald
netfrc = 0,
skin_permit = 0.75,
&end
/
Cheers,
Piia
--
Piia Bartoš, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 |
piia.bartos.uef.fi<mailto:
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Received on Mon May 22 2023 - 23:30:03 PDT
