I see multiple possible issues in the output (net charge, contacts, etc)
but if you want to check if the bond is properly included, use parmed and
the "checkbonds" command.
the phosaa library won't help since you should have everything you need in
your frcmod and gaff files. You didn't mention the ligand library setup
though, if the bond is missing you might need to check that part.
On Tue, Feb 27, 2024 at 1:49 PM Cao, Dillon P. via AMBER <amber.ambermd.org>
wrote:
> I am doing a simulation of a protein and a covalently-linked
> methylphosphonate inhibitor. During the simulation, the methyl C and P bond
> of the inhibitor fluctuates between 1.8 angstroms to 4 angstroms. I
> obtained the nonstandard parameters through Gaussian ESP calculations.
> During tleap, I did not get any warnings about long bond length and
> checking the initial prmtop and rst7 files in pyMOL showed the correct bond
> length of 1.8 angstroms, but the phosphorous atom white seemingly
> unrecognized (the saved pdb from tleap correctly recognizes the phosphorus
> and colors it orange). The bond stretched bond length was first noticed
> right after the equilibrium steps (frame 1 of my production run). Should I
> have loaded the leaprc.phosaa14SB force field?
>
> The force fields parameters loaded were :
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> source leaprc.gaff2
>
> Other parameters I loaded were:
> loadamberparams frcmod.ionsjc_tip3p
> set default PBradii mbondi3
> *I also loaded the frcmod files I generated for the nonstandard residue
>
> Here is the end of the leap file when I saved the topology:
>
> Warning: Converting N-terminal residue name to PDB format: NGLU -> GLU
>
> Warning: Converting C-terminal residue name to PDB format: CGLU -> GLU
>
> Warning: Converting C-terminal residue name to PDB format: CPRO -> PRO
>
> Warning: Converting N-terminal residue name to PDB format: NGLY -> GLY
>
> Warning: Converting C-terminal residue name to PDB format: CPRO -> PRO
>
> Warning: Converting N-terminal residue name to PDB format: NPRO -> PRO
>
> Warning: Converting C-terminal residue name to PDB format: CALA -> ALA
> > charge solvcomplex
> Total unperturbed charge: -0.206999
> Total perturbed charge: -0.206999
> > check solvcomplex
> Checking 'solvcomplex'....
> Warning: The unperturbed charge of the unit (-0.206999) is not integral.
>
> Warning: The unperturbed charge of the unit (-0.206999) is not zero.
>
> Warning: Close contact of 1.491 angstroms between nonbonded atoms H and OD1
> ------- .R<TRP 491>.A<H 2> and .R<ASN 483>.A<OD1 9>
>
> Warning: Close contact of 1.285 angstroms between nonbonded atoms HD3 and
> HB2
> ------- .R<CPRO 256>.A<HD3 4> and .R<PRO 255>.A<HB2 9>
>
> Warning: Close contact of 1.461 angstroms between nonbonded atoms HH and
> OD2
> ------- .R<TYR 102>.A<HH 15> and .R<ASP 2>.A<OD2 10>
>
> Warning: Close contact of 1.132 angstroms between nonbonded atoms HE2 and
> H20
> ------- .R<TYR 69>.A<HE2 17> and .R<LIG 534>.A<H20 50>
>
> Warning: Close contact of 1.442 angstroms between nonbonded atoms HG3 and
> HH21
> ------- .R<GLU 48>.A<HG3 10> and .R<ARG 42>.A<HH21 21>
>
> Warning: Close contact of 1.455 angstroms between nonbonded atoms H and
> HG22
> ------- .R<GLY 23>.A<H 2> and .R<THR 21>.A<HG22 9>
> Checking parameters for unit 'solvcomplex'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 8
> Unit is OK.
>
> Sincerely,
> Dillon
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Received on Tue Feb 27 2024 - 14:30:02 PST
