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
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Received on Mon Dec 13 2021 - 14:30:03 PST
