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?
This email may contain proprietary, confidential and/or privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender by reply email and delete all copies of this message.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 06 2022 - 10:30:02 PST
