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Cleaned emref module and adapted other to new env variables #140

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Nov 24, 2021
Merged

Cleaned emref module and adapted other to new env variables #140

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6ff370a
Cleaned emref module and adapted other to new env variables
amjjbonvin Nov 23, 2021
043b165
removes print. Closes #141
joaomcteixeira Nov 24, 2021
0b76784
corrects ambig_fname var names
joaomcteixeira Nov 24, 2021
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4 changes: 1 addition & 3 deletions examples/docking/docking.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -43,11 +43,9 @@ ambig_fname = '../data/1a2k_ti.tbl'
cool1_steps = 500
noecv = true

[mdref]
[emref]
ambig_fname = '../data/1a2k_ti.tbl'
cool1_steps = 10
noecv = true
solvshell = false

# ====================================================================

0 ...ent/flexref/cns/toppar/carbohydrate.param → src/haddock/cns/toppar/carbohydrate.param
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0 ...pology/topoaa/cns/toppar/carbohydrate.top → src/haddock/cns/toppar/carbohydrate.top
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0 ...pology/topoaa/cns/toppar/dna-rna-1.3.link → src/haddock/cns/toppar/dna-rna-1.3.link
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13 changes: 13 additions & 0 deletions src/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p-break.top
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@@ -0,0 +1,13 @@
PRESidue DNCG
! patch for deletion of nucleic acid linkage
! that are too long to exist

DELETE BOND +BB3 -BB1
DELETE ANGLE -BB2 -BB3 +BB1
DELETE ANGLE -BB3 +BB1 +BB2
DELETE DIHEdral -BB1 -BB2 -BB3 +BB1
DELETE DIHEdral -BB2 -BB3 +BB1 +BB2
DELETE DIHEdral -BB3 +BB1 +BB2 +BB3
DELETE ANGLE -SC1 -BB3 +BB1

END {DNCG}
48 changes: 48 additions & 0 deletions src/haddock/cns/toppar/dna-rna-CG-MARTINI-2-1p.link
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@@ -0,0 +1,48 @@
remarks this is a macro to define cg nucleid acid links

set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result)
set message=off echo=off end

checkversion 1.3

link nuc head - DA tail + DA end
link nuc head - DA tail + DC end
link nuc head - DA tail + DG end
link nuc head - DA tail + DT end

link nuc head - DC tail + DA end
link nuc head - DC tail + DC end
link nuc head - DC tail + DG end
link nuc head - DC tail + DT end

link nuc head - DG tail + DA end
link nuc head - DG tail + DC end
link nuc head - DG tail + DG end
link nuc head - DG tail + DT end

link nuc head - DT tail + DA end
link nuc head - DT tail + DC end
link nuc head - DT tail + DG end
link nuc head - DT tail + DT end

link nuc head - A tail + A end
link nuc head - A tail + C end
link nuc head - A tail + G end
link nuc head - A tail + U end

link nuc head - C tail + A end
link nuc head - C tail + C end
link nuc head - C tail + G end
link nuc head - C tail + U end

link nuc head - G tail + A end
link nuc head - G tail + C end
link nuc head - G tail + G end
link nuc head - G tail + U end

link nuc head - U tail + A end
link nuc head - U tail + C end
link nuc head - U tail + G end
link nuc head - U tail + U end

set message=$old_message echo=$old_echo end
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