this tutorial has a section on determining how much salt to add. I think it
just covers Na+ and Cl-
https://ambermd.org/tutorials/basic/tutorial7/index.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
