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jayponderjayponder
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add water extra-site BIOTYPE; generalize TORTORS parameter format
1 parent f5f1bea commit 505368f

28 files changed

+7577
-21416
lines changed

‎params/amber14sb.prm‎

Lines changed: 15 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -4324,17 +4324,18 @@ biotype 1252 P "3'-Monophosphate P DNA" 999
43244324
biotype 1253 OP "3'-Monophosphate OP DNA" 1000
43254325
biotype 2001 O "Water" 1001
43264326
biotype 2002 H "Water" 1002
4327-
biotype 2003 LI "Lithium Ion" 1003
4328-
biotype 2004 NA "Sodium Ion" 1004
4329-
biotype 2005 K "Potassium Ion" 1005
4330-
biotype 2006 RB "Rubidium Ion" 1006
4331-
biotype 2007 CS "Cesium Ion" 1007
4332-
biotype 2008 MG "Magnesium Ion" 1008
4333-
biotype 2009 CA "Calcium Ion" 1009
4334-
biotype 2010 SR "Strontium Ion" 1010
4335-
biotype 2011 BA "Barium Ion" 1011
4336-
biotype 2012 F "Fluoride Ion" 1012
4337-
biotype 2013 CL "Chloride Ion" 1013
4338-
biotype 2014 BR "Bromide Ion" 1014
4339-
biotype 2015 I "Iodide Ion" 1015
4340-
biotype 2016 ZN "Zinc Ion" 1016
4327+
biotype 2003 EP "Water" 0
4328+
biotype 2004 LI "Lithium Ion" 1003
4329+
biotype 2005 NA "Sodium Ion" 1004
4330+
biotype 2006 K "Potassium Ion" 1005
4331+
biotype 2007 RB "Rubidium Ion" 1006
4332+
biotype 2008 CS "Cesium Ion" 1007
4333+
biotype 2009 MG "Magnesium Ion" 1008
4334+
biotype 2010 CA "Calcium Ion" 1009
4335+
biotype 2011 SR "Strontium Ion" 1010
4336+
biotype 2012 BA "Barium Ion" 1011
4337+
biotype 2013 F "Fluoride Ion" 1012
4338+
biotype 2014 CL "Chloride Ion" 1013
4339+
biotype 2015 BR "Bromide Ion" 1014
4340+
biotype 2016 I "Iodide Ion" 1015
4341+
biotype 2017 ZN "Zinc Ion" 1016

‎params/amber94.prm‎

Lines changed: 15 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -3691,13 +3691,18 @@ biotype 1252 P "3'-Monophosphate P DNA" 1252
36913691
biotype 1253 OP "3'-Monophosphate OP DNA" 1253
36923692
biotype 2001 O "Water" 2001
36933693
biotype 2002 H "Water" 2002
3694-
biotype 2003 LI "Lithium Ion" 2003
3695-
biotype 2004 NA "Sodium Ion" 2004
3696-
biotype 2005 K "Potassium Ion" 2005
3697-
biotype 2006 RB "Rubidium Ion" 2006
3698-
biotype 2007 CS "Cesium Ion" 2007
3699-
biotype 2008 MG "Magnesium Ion" 2008
3700-
biotype 2009 CA "Calcium Ion" 2009
3701-
biotype 2010 SR "Strontium Ion" 2010
3702-
biotype 2011 BA "Barium Ion" 2011
3703-
biotype 2013 CL "Chloride Ion" 2012
3694+
biotype 2003 EP "Water" 0
3695+
biotype 2004 LI "Lithium Ion" 2003
3696+
biotype 2005 NA "Sodium Ion" 2004
3697+
biotype 2006 K "Potassium Ion" 2005
3698+
biotype 2007 RB "Rubidium Ion" 2006
3699+
biotype 2008 CS "Cesium Ion" 2007
3700+
biotype 2009 MG "Magnesium Ion" 2008
3701+
biotype 2010 CA "Calcium Ion" 2009
3702+
biotype 2011 SR "Strontium Ion" 2010
3703+
biotype 2012 BA "Barium Ion" 2011
3704+
biotype 2013 F "Fluoride Ion" -1
3705+
biotype 2014 CL "Chloride Ion" 2012
3706+
biotype 2015 BR "Bromide Ion" -1
3707+
biotype 2016 I "Iodide Ion" -1
3708+
biotype 2017 ZN "Zinc Ion" -1

‎params/amber96.prm‎

Lines changed: 15 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -3720,13 +3720,18 @@ biotype 1252 P "3'-Monophosphate P DNA" 1252
37203720
biotype 1253 OP "3'-Monophosphate OP DNA" 1253
37213721
biotype 2001 O "Water" 2001
37223722
biotype 2002 H "Water" 2002
3723-
biotype 2003 LI "Lithium Ion" 2003
3724-
biotype 2004 NA "Sodium Ion" 2004
3725-
biotype 2005 K "Potassium Ion" 2005
3726-
biotype 2006 RB "Rubidium Ion" 2006
3727-
biotype 2007 CS "Cesium Ion" 2007
3728-
biotype 2008 MG "Magnesium Ion" 2008
3729-
biotype 2009 CA "Calcium Ion" 2009
3730-
biotype 2010 SR "Strontium Ion" 2010
3731-
biotype 2011 BA "Barium Ion" 2011
3732-
biotype 2013 CL "Chloride Ion" 2012
3723+
biotype 2003 EP "Water" 0
3724+
biotype 2004 LI "Lithium Ion" 2003
3725+
biotype 2005 NA "Sodium Ion" 2004
3726+
biotype 2006 K "Potassium Ion" 2005
3727+
biotype 2007 RB "Rubidium Ion" 2006
3728+
biotype 2008 CS "Cesium Ion" 2007
3729+
biotype 2009 MG "Magnesium Ion" 2008
3730+
biotype 2010 CA "Calcium Ion" 2009
3731+
biotype 2011 SR "Strontium Ion" 2010
3732+
biotype 2012 BA "Barium Ion" 2011
3733+
biotype 2013 F "Fluoride Ion" -1
3734+
biotype 2014 CL "Chloride Ion" 2012
3735+
biotype 2015 BR "Bromide Ion" -1
3736+
biotype 2016 I "Iodide Ion" -1
3737+
biotype 2017 ZN "Zinc Ion" -1

‎params/amber98.prm‎

Lines changed: 15 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -3729,13 +3729,18 @@ biotype 1252 P "3'-Monophosphate P DNA" 1252
37293729
biotype 1253 OP "3'-Monophosphate OP DNA" 1253
37303730
biotype 2001 O "Water" 2001
37313731
biotype 2002 H "Water" 2002
3732-
biotype 2003 LI "Lithium Ion" 2003
3733-
biotype 2004 NA "Sodium Ion" 2004
3734-
biotype 2005 K "Potassium Ion" 2005
3735-
biotype 2006 RB "Rubidium Ion" 2006
3736-
biotype 2007 CS "Cesium Ion" 2007
3737-
biotype 2008 MG "Magnesium Ion" 2008
3738-
biotype 2009 CA "Calcium Ion" 2009
3739-
biotype 2010 SR "Strontium Ion" 2010
3740-
biotype 2011 BA "Barium Ion" 2011
3741-
biotype 2013 CL "Chloride Ion" 2012
3732+
biotype 2003 EP "Water" 0
3733+
biotype 2004 LI "Lithium Ion" 2003
3734+
biotype 2005 NA "Sodium Ion" 2004
3735+
biotype 2006 K "Potassium Ion" 2005
3736+
biotype 2007 RB "Rubidium Ion" 2006
3737+
biotype 2008 CS "Cesium Ion" 2007
3738+
biotype 2009 MG "Magnesium Ion" 2008
3739+
biotype 2010 CA "Calcium Ion" 2009
3740+
biotype 2011 SR "Strontium Ion" 2010
3741+
biotype 2012 BA "Barium Ion" 2011
3742+
biotype 2013 F "Fluoride Ion" -1
3743+
biotype 2014 CL "Chloride Ion" 2012
3744+
biotype 2015 BR "Bromide Ion" -1
3745+
biotype 2016 I "Iodide Ion" -1
3746+
biotype 2017 ZN "Zinc Ion" -1

‎params/amber99.prm‎

Lines changed: 15 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -3696,13 +3696,18 @@ biotype 1252 P "3'-Monophosphate P DNA" 1252
36963696
biotype 1253 OP "3'-Monophosphate OP DNA" 1253
36973697
biotype 2001 O "Water" 2001
36983698
biotype 2002 H "Water" 2002
3699-
biotype 2003 LI "Lithium Ion" 2003
3700-
biotype 2004 NA "Sodium Ion" 2004
3701-
biotype 2005 K "Potassium Ion" 2005
3702-
biotype 2006 RB "Rubidium Ion" 2006
3703-
biotype 2007 CS "Cesium Ion" 2007
3704-
biotype 2008 MG "Magnesium Ion" 2008
3705-
biotype 2009 CA "Calcium Ion" 2009
3706-
biotype 2010 SR "Strontium Ion" 2010
3707-
biotype 2011 BA "Barium Ion" 2011
3708-
biotype 2013 CL "Chloride Ion" 2012
3699+
biotype 2003 EP "Water" 0
3700+
biotype 2004 LI "Lithium Ion" 2003
3701+
biotype 2005 NA "Sodium Ion" 2004
3702+
biotype 2006 K "Potassium Ion" 2005
3703+
biotype 2007 RB "Rubidium Ion" 2006
3704+
biotype 2008 CS "Cesium Ion" 2007
3705+
biotype 2009 MG "Magnesium Ion" 2008
3706+
biotype 2010 CA "Calcium Ion" 2009
3707+
biotype 2011 SR "Strontium Ion" 2010
3708+
biotype 2012 BA "Barium Ion" 2011
3709+
biotype 2013 F "Fluoride Ion" -1
3710+
biotype 2014 CL "Chloride Ion" 2012
3711+
biotype 2015 BR "Bromide Ion" -1
3712+
biotype 2016 I "Iodide Ion" -1
3713+
biotype 2017 ZN "Zinc Ion" -1

‎params/amber99sb.prm‎

Lines changed: 15 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -3700,13 +3700,18 @@ biotype 1252 P "3'-Monophosphate P DNA" 1252
37003700
biotype 1253 OP "3'-Monophosphate OP DNA" 1253
37013701
biotype 2001 O "Water" 2001
37023702
biotype 2002 H "Water" 2002
3703-
biotype 2003 LI "Lithium Ion" 2003
3704-
biotype 2004 NA "Sodium Ion" 2004
3705-
biotype 2005 K "Potassium Ion" 2005
3706-
biotype 2006 RB "Rubidium Ion" 2006
3707-
biotype 2007 CS "Cesium Ion" 2007
3708-
biotype 2008 MG "Magnesium Ion" 2008
3709-
biotype 2009 CA "Calcium Ion" 2009
3710-
biotype 2010 SR "Strontium Ion" 2010
3711-
biotype 2011 BA "Barium Ion" 2011
3712-
biotype 2013 CL "Chloride Ion" 2012
3703+
biotype 2003 EP "Water" 0
3704+
biotype 2004 LI "Lithium Ion" 2003
3705+
biotype 2005 NA "Sodium Ion" 2004
3706+
biotype 2006 K "Potassium Ion" 2005
3707+
biotype 2007 RB "Rubidium Ion" 2006
3708+
biotype 2008 CS "Cesium Ion" 2007
3709+
biotype 2009 MG "Magnesium Ion" 2008
3710+
biotype 2010 CA "Calcium Ion" 2009
3711+
biotype 2011 SR "Strontium Ion" 2010
3712+
biotype 2012 BA "Barium Ion" 2011
3713+
biotype 2013 F "Fluoride Ion" -1
3714+
biotype 2014 CL "Chloride Ion" 2012
3715+
biotype 2015 BR "Bromide Ion" -1
3716+
biotype 2016 I "Iodide Ion" -1
3717+
biotype 2017 ZN "Zinc Ion" -1

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