Hi Carlos,
Thank you for your suggestion. It pointed me in the right direction. The issue was I had "ATTN" lines that was inputs of 0 in my ff14SB frcmod file. In addition to this, I was loading that second after my gaff frcmod file which made the ATTN lines take precedent over my gaff frcmod.
I solved it by removing the ATTN lines.
Here is my prmtop file from parmed before
>printBonds :200
3073 C12 ( CT) 3053 P1 ( P) 0.0000 0.0000
>printAngles :200
3074 H19 ( HC) 3073 C12 ( CT) 3053 P1 ( P) 0.0000 0.0000
3075 H20 ( HC) 3073 C12 ( CT) 3053 P1 ( P) 0.0000 0.0000
3075 H20 ( HC) 3073 C12 ( CT) 3074 H19 ( HC) 35.0000 109.5000
3076 H21 ( HC) 3073 C12 ( CT) 3053 P1 ( P) 0.0000 0.0000
3076 H21 ( HC) 3073 C12 ( CT) 3074 H19 ( HC) 35.0000 109.5000
3076 H21 ( HC) 3073 C12 ( CT) 3075 H20 ( HC) 35.0000 109.5000
Here it is after I regenerated the topology files:
>printBonds :200
3073 C12 ( CT) 3053 P1 ( P) 1.8390 243.3000
>printAngles :200
3074 H19 ( HC) 3073 C12 ( CT) 3053 P1 ( P) 53.3000 108.4300
3075 H20 ( HC) 3073 C12 ( CT) 3053 P1 ( P) 53.3000 108.4300
3075 H20 ( HC) 3073 C12 ( CT) 3074 H19 ( HC) 39.4000 107.5800
3076 H21 ( HC) 3073 C12 ( CT) 3053 P1 ( P) 53.3000 108.4300
3076 H21 ( HC) 3073 C12 ( CT) 3074 H19 ( HC) 39.4000 107.5800
3076 H21 ( HC) 3073 C12 ( CT) 3075 H20 ( HC) 39.4000 107.5800
Sincerely,
Dillon
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Tuesday, February 27, 2024 4:10 PM
To: Cao, Dillon P. <dillon.cao.swri.org>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Long Bond length during simulation of nonstandard residue
[EXTERNAL EMAIL]
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<mailto: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 - 15:30:02 PST
