Hi
You can try using a non hydrogen added structure to run tleap and see what
you get. And for this particular residue, you can try using only the
backbone atoms. May be it can solve the problem.
Best
Suchetana
On Tue, Dec 6, 2022 at 10:00 AM Gonzalo R. Vazquez-Jimenez via AMBER <
amber.ambermd.org> wrote:
> Hi everyone, this is my first post using the AMBER mailing list.
>
> I am trying to simulate WT alpha synuclein using a pdb file, which I made
> using the amino acid sequence found on its FASTA page via molefacture on
> VMD. I was successfully able to make the pdb and convert it to an
> AMBER-friendly version using pdb4amber. Now I am trying to use tleap to
> make the appropriate parameter and restart files for future MD simulations.
> After I load the pdb, I get the message found below. For context, I am
> running amber22.
>
> ...
> Added missing heavy atom: .R<CMET 1>.A<OXT 18>
> total atoms in file: 2020
> Leap added 3 missing atoms according to residue templates:
> 1 Heavy
> 2 H / lone pairs
> The file contained 1997 atoms not in residue templates
>
> How can this be fixed? I tried following the AMBER tutorial "1.2
> Fundamentals of LEaP", however whenever I follow those steps, I end up
> getting an error such as the following for every atom in the system, when I
> try make the files.
>
> FATAL: Atom .R<CMET 1>.A<HC1 2015> does not have a type.
>
> For context, I am trying to simulate this system in the gas phase, however
> I have tried solvating it on tleap, but I still get the same message either
> way. I have also tried performing this on much simpler systems such as
> trialanine to try troubleshooting any potentially obvious issues, however I
> have not had much luck. Any help on this situation would be highly
> appreciated as I have been stumped on this for weeks.
>
> PS: According to the LEaP page on the AMBER website, .top and .crd files
> are favorable, but would it also be possible to obtain .parm7 and .rst7
> files without using CHARMM or gromacs?
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Received on Tue Dec 06 2022 - 10:30:03 PST
