On Tue, Dec 06, 2022, Gonzalo R. Vazquez-Jimenez via AMBER wrote:
>
>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.
>Added missing heavy atom: .R<CMET 1>.A<OXT 18>
This is a very odd message: it indicates that the program thinks residue 1
is a C-terminal residue, and is trying to add an OXT atom, which would be
normal for a true C-terminal residue.
Look carefully at your PDB file, especially right at the beginning. If you
can't figure this out, you may need to post the file. (Aside: is there a
reason that you want to use a molefacture structure?)
>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.
We would have to know lots more information here. Is this still the same
input PDB file? What was different between the first run and the second?
You may need to post the exact commands you used in tleap.
>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?
This is an odd question. I'm unsure what you mean by "the LEaP page on the
Amber website." That aside, Amber users rarely use CHARMM or gromacs at
all. The tleap program is designed to create topology and coordinate files,
starting from a (good) PDB file as input.
...good luck...dac
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Received on Wed Dec 07 2022 - 07:00:02 PST
