[AMBER] tleap parameter file

From: Mac Kevin Braza via AMBER <amber.ambermd.org>
Date: Fri, 20 Jan 2023 13:52:00 -0800

Hello AMBER team,

I would like to ask for help in preparing my structure's prmtop and crd

This is the error that I am encountering with AMBER 22 tleap

  total atoms in file: 6314
  Leap added 6 missing atoms according to residue templates:
       6 H / lone pairs
  The file contained 2 atoms not in residue templates
Checking Unit.

/software/repo/moleculardynamics/amber/2022/bin/teLeap: Warning!
The unperturbed charge of the unit (-6.000400) is not zero.

/software/repo/moleculardynamics/amber/2022/bin/teLeap: Warning!
The perturbed charge (-6.000400) is not zero.
FATAL: Atom .R<NALA 67>.A<H 13> does not have a type.
FATAL: Atom .R<NALA 254>.A<H 13> does not have a type.

/software/repo/moleculardynamics/amber/2022/bin/teLeap: Fatal Error!
Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0.

I am using this script for tleap

source leaprc.protein.ff14SB
source leaprc.gaff
loadamberparams frcmod.ionsjc_tip3p
loadamberparams frcmod.zinc
loadoff znb.lib
loadoff hin.lib
loadoff hydroxide.lib

a=loadpdb protein.pdb
saveamberparm a protein.crd
savepdb a protein_v2.pdb

I am wondering if I can use some other library to make sure that the NALA
residues are being recognized. Also, is this an issue with AMBER22
specifically? My colleague who used a previous version of tleap was able to
use it. But now all I have is AMBER 22 tleap program. I also attached the
protein structure. Thank you!


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Received on Fri Jan 20 2023 - 14:00:04 PST
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