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 - 14:00:03 PST
