Liu Shiyong wrote:
Fatal error:
atoms 4176 and 4182 in charge group 1767 are in different energy groups
PDB:
ATOM 4176 OG SER A 541 -13.599 44.346 39.228 1.00 0.00
S 1
ATOM 4177 N ALA A 542 -12.827 48.211 42.079 1.00 0.00
A 1
ATOM 4178 CA ALA A 542 -12.788 48.960 43.342 1.00 0.00
A 1
ATOM 4179 C ALA A 542 -12.052 50.279 43.097 1.00 0.00
A 1
ATOM 4180 O ALA A 542 -12.096 50.830 41.993 1.00 0.00
A 1
ATOM 4181 CB ALA A 542 -12.084 48.160 44.447 1.00 0.00
A 1
ATOM 1 N THR B 1 22.984 77.078 8.100 1.00 20.55
T N
Using a structure file to understand a topology problem will give you nothing
useful. Charge groups are spelled out in the .top, so look there. I suspect
you are once again using the wrong structure file for whatever you're doing.
This .pdb file does not have any hydrogens, which means that this structure was
not processed by pdb2gmx under any force field (even a UA one), and thus will
not correspond to your topology whatsoever.
-Justin
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu <mailto:sy...@ku.edu> (shiyong...@ku.edu
<mailto:shiyong...@ku.edu> or liushiy...@ku.edu <mailto:liushiy...@ku.edu>)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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