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Link Information not getting reflected in itp file #415
- subha
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2 years 2 weeks ago #9374
by subha
Link Information not getting reflected in itp file #415 was created by subha
Hi,
So I was defining link information for backbone bonds, angles and dihedrals under the link directive as follows but this information do not show up in the molecule.itp file. Is this a bug or am I doing something wrong with the definitions:
;;;; Links
;; Links for COIL. We apply them first as coil is the default.
[ link ]
resname $na_resnames
[ bonds ]
BB1 BB2 1 0.363 20000 {"group": "Backbone bonds"}
BB2 BB3 1 0.202 40000 {"group": "Backbone bonds"}
BB3 +BB1 1 0.354 10000 {"group": "Backbone bonds"}
-BB3 BB1 1 0.354 10000 {"group": "Backbone bonds"}
[ link ]
resname $na_resnames
[ angles ]
#meta {"group": "BBB angles"}
BB1 BB2 BB3 2 117 175 {"group": "BBB angles", "comment": "BB1-BB2-BB3"}
BB2 BB3 +BB1 2 95 105 {"group": "BBB angles", "comment": "BB2-BB3-BB1"}
-BB2 -BB3 BB1 2 95 105 {"group": "BBB angles", "comment": "BB2-BB3-BB1"}
BB3 +BB1 +BB2 2 93 75 {"group": "BBB angles", "comment": "BB3-BB1-BB2"}
-BB3 BB1 BB2 2 93 75 {"group": "BBB angles", "comment": "BB3-BB1-BB2"}
[ link ]
resname $na_resnames
[dihedrals]
#meta {"group": "BB-BB-BB-BB"}
BB1 BB2 BB3 +BB1 2 0 3.5 1 {"group": "BB-BB-BB-BB"}
BB2 BB3 +BB1 +BB2 1 0.0 1 4 {"group": "BB-BB-BB-BB"}
BB3 +BB1 +BB2 +BB3 9 -10.0 1.5 2 {"group": "BB-BB-BB-BB"}
BB3 +BB1 +BB2 +BB3 9 10.0 1.5 2 {"group": "BB-BB-BB-BB"}
-BB3 BB1 BB2 BB3 9 10.0 1.5 2 {"group": "BB-BB-BB-BB"}
-BB3 BB1 BB2 BB3 9 -10.0 1.5 2 {"group": "BB-BB-BB-BB"}
-BB2 -BB3 BB1 BB2 1 0.0 1 4 {"group": "BB-BB-BB-BB"}
-BB1 -BB2 -BB3 BB1 2 0 3.5 1 {"group": "BB-BB-BB-BB"}
So I was defining link information for backbone bonds, angles and dihedrals under the link directive as follows but this information do not show up in the molecule.itp file. Is this a bug or am I doing something wrong with the definitions:
;;;; Links
;; Links for COIL. We apply them first as coil is the default.
[ link ]
resname $na_resnames
[ bonds ]
BB1 BB2 1 0.363 20000 {"group": "Backbone bonds"}
BB2 BB3 1 0.202 40000 {"group": "Backbone bonds"}
BB3 +BB1 1 0.354 10000 {"group": "Backbone bonds"}
-BB3 BB1 1 0.354 10000 {"group": "Backbone bonds"}
[ link ]
resname $na_resnames
[ angles ]
#meta {"group": "BBB angles"}
BB1 BB2 BB3 2 117 175 {"group": "BBB angles", "comment": "BB1-BB2-BB3"}
BB2 BB3 +BB1 2 95 105 {"group": "BBB angles", "comment": "BB2-BB3-BB1"}
-BB2 -BB3 BB1 2 95 105 {"group": "BBB angles", "comment": "BB2-BB3-BB1"}
BB3 +BB1 +BB2 2 93 75 {"group": "BBB angles", "comment": "BB3-BB1-BB2"}
-BB3 BB1 BB2 2 93 75 {"group": "BBB angles", "comment": "BB3-BB1-BB2"}
[ link ]
resname $na_resnames
[dihedrals]
#meta {"group": "BB-BB-BB-BB"}
BB1 BB2 BB3 +BB1 2 0 3.5 1 {"group": "BB-BB-BB-BB"}
BB2 BB3 +BB1 +BB2 1 0.0 1 4 {"group": "BB-BB-BB-BB"}
BB3 +BB1 +BB2 +BB3 9 -10.0 1.5 2 {"group": "BB-BB-BB-BB"}
BB3 +BB1 +BB2 +BB3 9 10.0 1.5 2 {"group": "BB-BB-BB-BB"}
-BB3 BB1 BB2 BB3 9 10.0 1.5 2 {"group": "BB-BB-BB-BB"}
-BB3 BB1 BB2 BB3 9 -10.0 1.5 2 {"group": "BB-BB-BB-BB"}
-BB2 -BB3 BB1 BB2 1 0.0 1 4 {"group": "BB-BB-BB-BB"}
-BB1 -BB2 -BB3 BB1 2 0 3.5 1 {"group": "BB-BB-BB-BB"}
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- subha
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2 years 1 week ago #9375
by subha
Replied by subha on topic Link Information not getting reflected in itp file #415
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- riccardo
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2 years 1 week ago #9376
by riccardo
Replied by riccardo on topic Link Information not getting reflected in itp file #415
thanks for linking this to the corresponding github issue!
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