Hi
I saw a similar post recently in the forum and I think as per David's
suggestion there, you could remove the hydrogens from the terminal residues
and let LEaP add them back.
On Fri, Jan 20, 2023 at 1:52 PM Mac Kevin Braza via AMBER <amber.ambermd.org>
wrote:
> Hello AMBER team,
>
> I would like to ask for help in preparing my structure's prmtop and crd
> files.
>
> 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
> quit
>
> 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!
>
> Sincerely,
> Kevin
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Received on Fri Jan 20 2023 - 14:30:03 PST
