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 - 11:00:02 PST
