[AMBER] Custom AA residue missing parameters

From: Javier O Sanlley-hernandez via AMBER <amber.ambermd.org>
Date: Mon, 19 Aug 2024 19:39:45 +0000

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 - 13:00:02 PDT
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