Hi,
I think if you generate parameters with parmchk2 you have to load
leaprc.gaff2 (not leaprc.gaff).
-Dan
On Mon, Aug 19, 2024 at 3:39 PM Javier O Sanlley-hernandez via AMBER
<amber.ambermd.org> wrote:
>
> Hello,
>
> I am trying to prepare a custom amino acid residue where a cysteine is covalently bound to a ligand for MD simulations.
>
> I followed the steps outlined in the amber custom amino acid residue<https://ambermd.org/tutorials/basic/tutorial5/> and tert-leucine tutorials<https://carlosramosg.com/amber-custom-residue-parameterization> supplemented by the documentation in the Amber 22 manual to generate the appropriate files. Commands are included below.
>
> The issue I’m having is that upon generating the necessary .prepin and .frcmod files, I cannot generate the .prmtop topology file when I run tleap using a pdb with the custom amino acid flanked by adjacent residues as input (Error: missing bond and angle parameters). Alternatively, running tleap with the uncapped residue pdb as input does not give me any errors.
>
> I also noticed that running the desc command on the custom residue shows ‘null’ for the head atom, even though both head and tail atoms were defined in the .mc file.
>
> Thanks in advance for your help,
>
> Javier Sanlley
> UC San Diego
>
> ---
>
> Amber22 commands:
>
> antechamber -i lig_capped.pdb -fi mol2 -o lig_capped.ac -fo ac -c bcc -rn LIG -at gaff
>
> prepgen -i lig_capped.ac -o lig_capped.prepin -f ac -m lig_capped.mc -rn LIG
>
> parmchk2 -i lig_capped.ac -o lig_capped.frcmod -f ac -a Y
> (no ATTN remarks)
>
> tleap input file
>
> Source leaprc.protein.ff19SB
> Source leaprc.gaff
>
> Loadamberprep lig_capped.prepin
> Loadamberparams lig_capped.frcmod
>
> LIG = loadpdb lig_uncapped.pdb or lig_flanked.pdb
>
> Saveoff LIG lig_uncapped.lib
> Saveamberparm LIG lig_uncapped.prmtop lig_uncapped.rst7
>
> Tleap error messages:
>
> Error: Could not find bond parameter for atom types: C - n
> for atom C at position -14.036000, 22.450000, -31.516000
> and atom N at position -14.822000, 21.367000, -31.604000.
>
> Error: Could not find bond parameter for atom types: c - N
> for atom C at position -13.727000, 20.025000, -33.379000
> and atom N at position -12.634000, 19.262000, -33.506000.
> Checking for angle parameters.
>
> Error: Could not find angle parameter for atom types: O - C - n
> for atom O at position -12.834000, 22.442000, -31.769000,
> atom C at position -14.036000, 22.450000, -31.516000,
> and atom N at position -14.822000, 21.367000, -31.604000.
>
> Error: Could not find angle parameter for atom types: C - n - hn
> for atom C at position -14.036000, 22.450000, -31.516000,
> atom N at position -14.822000, 21.367000, -31.604000,
> and atom H at position -15.804000, 21.448000, -31.377000.
>
> Error: Could not find angle parameter for atom types: C - n - c3
> for atom C at position -14.036000, 22.450000, -31.516000,
> atom N at position -14.822000, 21.367000, -31.604000,
> and atom CA at position -14.366000, 20.032000, -31.985000.
>
> Error: Could not find angle parameter for atom types: CX - C - n
> for atom CA at position -14.678000, 23.764000, -31.044000,
> atom C at position -14.036000, 22.450000, -31.516000,
> and atom N at position -14.822000, 21.367000, -31.604000.
>
> Error: Could not find angle parameter for atom types: o - c - N
> for atom O at position -14.193000, 20.727000, -34.274000,
> atom C at position -13.727000, 20.025000, -33.379000,
> and atom N at position -12.634000, 19.262000, -33.506000.
>
> Error: Could not find angle parameter for atom types: c - N - H
> for atom C at position -13.727000, 20.025000, -33.379000,
> atom N at position -12.634000, 19.262000, -33.506000,
> and atom H at position -12.326000, 18.698000, -32.725000.
>
> Error: Could not find angle parameter for atom types: c - N - CX
> for atom C at position -13.727000, 20.025000, -33.379000,
> atom N at position -12.634000, 19.262000, -33.506000,
> and atom CA at position -11.821000, 19.222000, -34.715000.
>
> Error: Could not find angle parameter for atom types: c3 - c - N
> for atom CA at position -14.366000, 20.032000, -31.985000,
> atom C at position -13.727000, 20.025000, -33.379000,
> and atom N at position -12.634000, 19.262000, -33.506000.
>
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Received on Mon Aug 19 2024 - 13:00:03 PDT
