Hi Christian, I don't have any solutions for you, but I can make a few
suggestions:
1) use the parmed program on your prmtop and use the "printdetails" command
to look a some parts (for example, printdetails :1-10). Does it look
reasonable?
2) make sure to look at your leap.log file when it loaded your PDB. There
will be a lot of useful info, especially about things that leap did not
recognize or did not match the libraries (for example, n-terminal MET does
not have an atom named HT1). If you don't have access to the log (because
of using CHARMM-GUI), then see the parmed suggestion above.
3) make a new PDB file that is much smaller as a test. Try keeping only the
first 100 or so atoms, and then process that one. If may be easier to see
what is happening
4) keep in mind the limits of standard PDB format, especially for very
large systems. Some programs will move the columns around once you have
more atoms than can fit, but that isn't allowed by PDB standard and I don't
know if CHARMM-GUI can process a PDB file with these changes.
carlos
On Fri, Nov 22, 2024 at 4:36 PM Christian Seitz via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I am trying to minimize a 3 million atom system in AMBER20 that was created
> through CHARMM-GUI. The CHARMM-GUI outputs had some issues and stopped
> numbering the atoms after a certain point, necessitating some manual edits
> and thus a potential source of error. I renumbered the atoms in my pdb
> file, and converted to parm7/rst7. When I try an initial minimization, I
> get this error, also shown in the attached error log:
>
> | ERROR: PMEMD does not support single H residues!
> | Atom number 1, Residue number 1
>
> However, my system is not meant to contain any single H residues and
> contains no dummy atoms. The pdb file is formatted like this (looks normal
> on terminal, :
> CRYST1 307.624 306.579 415.299 90.00 90.00 90.00 P 1 1
> ATOM 1 N MET X 1 -7.171 -15.622-119.707 1.00 0.00
> PROA
> ATOM 2 HT1 MET X 1 -6.809 -14.657-119.834 1.00 0.00
> PROA
>
> while the structure summary of the parm7 file is this:
> %FLAG POINTERS
> %FORMAT(10I8)
> 3276189 0 0 10 0 0 0 0 0
> 0
> 3276189 2252684 10 0 0 1 0 0 0
> 0
> 0 0 0 0 0 0 0 1 2854
> 0
> 0
>
> These files are 100-300 MB each but I can send Google drive links to them
> if necessary. Do you have any ideas or suggestions on what the error may
> be? Thanks in advance!
>
> Best,
> Christian
> --
> *Christian Seitz*
> PhD, Dept. of Computer Science | UChicago
> cgseitz.uchicago.edu
> [image: www.linkedin.com/in/christianseitz21]
> <http://www.linkedin.com/in/christianseitz21>
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Received on Fri Nov 22 2024 - 14:00:04 PST
