Thank you,
I've just finished reading it. And yes, unfortunately, they only cover Na+ and Cl-. I probably will do some research to see if there's any good paper on systems in PBS solvent simulation.
Yen Nguyen
Graduate Research Assistant
George Mason University
Department of Chemistry and Biochemistry
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Monday, December 13, 2021 5:31 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Peptide's charge is not 0 when getting parm7 and rst7 files
this tutorial has a section on determining how much salt to add. I think it
just covers Na+ and Cl-
https://secure-web.cisco.com/1WD8GVvvgFqQ1qXixm0FwMBIGganm8yOqjo6HoIjY2wp2E_rQOlJAuk3vYV3NBPrR-zAQ8HylEgiMcfMucqfuZQWC4REmaSbEtk41_biDAf25Tvw2pwxV7cZGkkXHBqbLFW7TLwgGKWYhyuDx4hAW6ekvv9B553Mf0XkkB_jyG9Ho3OLTq7LvAFoVEYpjbXl7Qyoc9bJ5WJJR640gHrqzzJl0D9dPHPNVkX8yKjWVZq8AtGWywI7xLTxOsfyabZAfx3I_jDWPOECNvyTPJEUCx82ZxLXzQo-rGIMDNn8ncWjlwHCZlyhYToBbYqBTd19jG_Pxu9BvoNuNb6nB49SeYMPdf4FDNwk-6VeMREQcVXz9P5ZNs1-TxYUOkuuHC54iUp6fYJ5QWzwWubWufb5qb_Jw3JbdFDwE71aJ6kyVCYJYVoC0TI_oMAoDwy7lPkxU/https%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial7%2Findex.php
On Mon, Dec 13, 2021 at 5:25 PM Yen Nguyen <ynguyen3.gmu.edu> wrote:
> Hi Carlos,
>
> Thank you so much for the response and the duplicated questions. I thought
> my original email didn't go through.
>
> There's another research group that would test my compound. I'm not sure
> what they would exactly add to my peptide when testing it. But it's likely
> a buffer like PBS (Phosphate-buffered saline). I want to do one simulation
> with just water as my peptide dissolves in water, and one in the buffer.
> But I don't know how to add the ions like phosphate and Na+ when solvating
> the system so that they are uniformly distributed in the water box.
>
> Could you please guide me on this or give me a link to a tutorial where
> they've done something similar?
>
> Thank you so much.
>
>
>
> Yen Nguyen
> Graduate Research Assistant
> George Mason University
> Department of Chemistry and Biochemistry
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Monday, December 13, 2021 5:15 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Peptide's charge is not 0 when getting parm7 and rst7
> files
>
> >
> >
> > res total affected
> >
> > ACE 1
> > NHE 1
> > )
> > (no restraints)
> >
>
> this is fine, there is no error and it is just saying they aren't connected
> at both sides.
>
> >
> > Should I fix the charge of the system so it is 0 before doing anything
> > else? Like try adding Cl- ion to neutralize it?
> >
>
> this is up to you, and not really about this specific system. People often
> add ions to neutralize the system, but it is not needed. You may also
> consider if you want extra ions for salt, but this is up to you and may
> depend on the conditions you are trying to model. Ions can be added in
> tleap. More info can be found in this tutorial:
>
> https://secure-web.cisco.com/1e13V7OhOzpEcZueACo89m87Ai4Hd6b9blrqgxA5gqFFCQ7AYNz1g8shhyHKoQZirscNnUOVRGdKxbXBKi3V3lLpdEsqFKJ-6FUm_faHg11JkxYvqyKudld-Pvag9mL0XpGclLmLS8OdztGYbeAME-IK1lDwFgYNA1KxSVX9LbpRwpbgMWnLmn_G3fy1HxlT8mkKdlOhjmxpAaJXJnsbs6EY341svEA8dCY8_GVjtUq_VJmLR4V-N51LnqmdE7CHR_59rwNnLM3vazbdua-W1GSBFbkEaVev2OvX4pr7wyTQIlfxknrNBDCjZmkyo75_A1Y3u7xm2oOFrs2GewP4N_mQypPVlyp6KKbgIyVrg5b2OnV2-TTD_miKiTVaoa1gxEfcL_l2Awb6cW3k58QhAMS2s-iDhTl-ngk82VMtJsf2akx7DDfKUMW-5TBoq6SJo/https%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial7%2Findex.php
>
>
>
> > I also don't know if the ACE 1 and NHE1 not being recognized is going to
> > cause a big problem in the simulation.
> >
> see above - it was recognized fine and there is no problem with this part.
>
> On Mon, Dec 13, 2021 at 5:14 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I replied to this earlier today, search your email and check your spam
> > folder
> >
> > On Mon, Dec 13, 2021 at 5:13 PM Yen Nguyen <ynguyen3.gmu.edu> wrote:
> >
> >> Hello,
> >>
> >> I tried building the structure from scratch in tleap using the following
> >> command
> >>
> >> AbSOD-15aa-modified = sequence { ACE TRP GLU HID ALA TYR TYR ILE ASP PHE
> >> ARG ASN LEU ARG PRO LYS NHE}
> >>
> >> and the output structure is correct when I viewed it in chimera.
> >>
> >> But when I tried to save the parm7 and rst7 files after solvating the
> >> peptide, I got these messages.
> >>
> >> saveamberparm AbSOD-15aa-modified parm7 rst7
> >> Checking Unit.
> >>
> >> Warning: The unperturbed charge of the unit (1.000000) is not zero.
> >>
> >> Note: Ignoring the warnings from Unit Checking.
> >>
> >> Building topology.
> >> Building atom parameters.
> >> Building bond parameters.
> >> Building angle parameters.
> >> Building proper torsion parameters.
> >> Building improper torsion parameters.
> >> total 73 improper torsions applied
> >> Building H-Bond parameters.
> >> Incorporating Non-Bonded adjustments.
> >> Not Marking per-residue atom chain types.
> >> Marking per-residue atom chain types.
> >> (Residues lacking connect0/connect1 -
> >> these don't have chain types marked:
> >>
> >> res total affected
> >>
> >> ACE 1
> >> NHE 1
> >> )
> >> (no restraints)
> >>
> >> Should I fix the charge of the system so it is 0 before doing anything
> >> else? Like try adding Cl- ion to neutralize it?
> >> I also don't know if the ACE 1 and NHE1 not being recognized is going to
> >> cause a big problem in the simulation.
> >>
> >> Thank you.
> >>
> >> Yen Nguyen
> >> Graduate Research Assistant
> >> George Mason University
> >> Department of Chemistry and Biochemistry
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >>
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> >>
> >
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Received on Mon Dec 13 2021 - 15:00:02 PST
