From NWChem
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| 1:43:00 PM PDT - Tue, Jul 31st 2012 |
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Hello all,
I was trying to prepare a fragment file for a heme. In the PDB, the four nitrogen atoms are named NA, NB, NC and ND. It seems NWCHEM keeps recognizing them as 'N A', 'N B', 'N C' and 'N D' therefore the job died since coordinates of these atoms cannot be found.
Coordinates missing for atom 464:HEM N A
Coordinates missing for atom 464:HEM N B
Coordinates missing for atom 464:HEM N C
Coordinates missing for atom 464:HEM N D
My input looks like:
start hem
prepare
source hem.pdb
new_top new_seq
new_rst
modify segment 1 quantum
update lists
ignore
write hem_ref.pdb
write hem_ref.rst
end
task prepare
and the PDB looks like:
ATOM 7563 NC HEM 464 37.018 35.000 37.138
.....
I tried change the atom name to N1C or NC1 or N1 but none of them works.
Any comments will be appreciated!
Best,
Yue
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Posts 11
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| 2:14:40 PM PST - Tue, Dec 4th 2012 |
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| Did you create your own hem.frg or hem.sgm? Please check if the atom names have been correctly defined in these files, as this is where the atom name printed as having missing coordinates is read.
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