Hi Winter,
I'm a beginner to GMX,
when I use the following command:
"pdb2gmx -f 1G1S.pdb -p gr.top -o gr.gro -missing"
Don't use '-missing'. Since you're a beginner you're not allowed to
(unless you get a permit for it from one of the developers).
"WARNING: atom CD not found in residue 72 while adding improper
This is the result of using '-missing'.
Fatal error:
Atom S in residue TYR 2 not found in rtp entry with 18 atoms
while sorting atoms"
How to solve this fatal error?
Well, as I recall, but I may need to check my biochemistry books here,
there's no S in tyrosine. Is this a modified residue, or is there just
something _else_ wrong with your starting structure? Note that I say
something else, since you clearly also have missing atoms, which you
need to fix. Go work on the starting structure!
Best,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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