gaff.prm and bondtyp.txt are updated in order to reproduce the atom types based on the Wang et al. Vol. 25, No. 9 . Journal of computational Chemistry. 2004

data/atomtyp.txt

@@ -40,17 +40,12 @@ INTHYB  [$([#8D1][#6][#8D1])]     2       #sp2 oxygen
 INTHYB  [$(O#*)]                  1       #sp  oxygen
 
 INTHYB  [P]                       3       #sp3 phosphorus
-INTHYB  [#15]                     3       #sp3 phosphorus
 INTHYB  [#15;$([PD1]=*)]          2       #sp2 phosphorus
-INTHYB  [P;$([PD1]=*)]            2       #sp2 phosphorusINTHYB  [PD5]			  5	  #sp3d phosphorus, as in PF5
+INTHYB  [PD5]			  5	  #sp3d phosphorus, as in PF5
 INTHYB  [Pv5]			  5	  #sp3d phosphorus, as in H3PO4
-INTHYB  [#15v5]			  5	  #sp3d phosphorus, as in H3PO4
 INTHYB  [S]                       3       #sp3 sulfur
-INTHYB  [#16]                     3       #sp3 sulfur
 INTHYB  [#16;s,$([SD1]=*)]        2       #sp2 sulfur
-INTHYB  [S;s,$([SD1]=*)]          2       #sp2 sulfur
 INTHYB  [SD6]			  6	  #sp3d2 sulfur, as in SF6
-INTHYB  [#16D6]			  6	  #sp3d2 sulfur, as in SF6
 INTHYB  [B]                       2       #sp2 boron
 INTHYB  [BD4]                     3       #sp3 boron
 
@@ -146,9 +141,7 @@ IMPVAL [#8^1+]                    1 # carbon monoxide
 IMPVAL [$([#8]#*)]                1
 
 IMPVAL  [#9D0]                    1
-IMPVAL  [FD0]                     1
 IMPVAL  [#9D0-]                   0 #[F-]
-IMPVAL  [FD0-]                    0 #[F-]
 
 IMPVAL  [#13]                     3 # generic Al
 
@@ -178,11 +171,8 @@ IMPVAL  [$([#16D3](=O)(=O)-O)]    4 #e.g. O[S](=O)=O
 IMPVAL  [$([#16D2](=O)-O)]        3 # e.g. O[S]=O
 IMPVAL  [#16D1-]                  1
 
-
-IMPVAL  [ClD0]                    1
 IMPVAL  [#17D0]                   1
 IMPVAL  [#17D0-]                  0 #[Cl-]
-IMPVAL  [ClD0-]                  0 #[Cl-]
 
 IMPVAL  [#31]                     3
 IMPVAL  [#32]                     4
@@ -193,20 +183,15 @@ IMPVAL  [as]                      3
 IMPVAL  [#34]                     2
 
 IMPVAL  [#35D0]                   1
-IMPVAL  [BrD0]                    1
 IMPVAL  [#35D0-]                  0 #[Br-]
-IMPVAL  [BrD0-]                   0 #[Br-]
 
 #IMPVAL  [#49,#81]                 3 # In, Tl, like Ga
 #IMPVAL  [#50,#82]                 4 # Sn, Pb, like Ge
 #IMPVAL  [#51,#83]                 3 # Sb, Bi, like As
 
-IMPVAL  [#53]                     2
-IMPVAL  [I]                       2
+IMPVAL  [#52]                     2
 IMPVAL  [#53D0]                   1
-IMPVAL  [ID0]                     1
 IMPVAL  [#53D0-]                  0 #[I-]
-IMPVAL  [ID0-]                    0 #[I-]
 
 #
 #EXTERNAL TYPE RULES

data/gaff.prm

@@ -14,7 +14,9 @@
 // [SMARTS] [atomtype id number] [description]
 // must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!
 //
-// Be careful lines do not exceed the maximum length of 80!
+// Upadted (2016) by Mohammad Mehdi Ghahremanpour <mohammad.ghahremanpour@icm.uu.se>
+//
+// Be careful lines do not exceed the maximum length of 150!
 
 
 // SMARTS rules for hydrogens
@@ -232,8 +234,8 @@ atom [#15;a]                  	     					    pb "aromatic P"
 atom [#15X3]                  						    p3 "other sp3 P"
 atom [#15X3](=*)-*=*          	     					    px "sp2 P of conjugated system"
 atom [#15X3](=*)-*#*          	     					    px "sp2 P of conjugated system"
+atom [#15X3](=[#8])(=[#8])[#8] 						    p4 ""
 atom [#15X3]=[O,S]            	     					    p4 "hypervalent P"
-atom [#15X3](=[#8])(=[#8])[#8] 						    p3 ""
 atom [#15X4]                  						    p5 "hypervalent P"
 atom [#15X4](=*)-*=*          						    py "P of conjugated system"
 atom [#15X4](=*)-*#*          	    					    py "P of conjugated system"
@@ -260,7 +262,7 @@ atom [#7X2;R](:[#6])[#7] 						    nd "sp2 N of conjugated ring"
 atom [#7X2;R]=[#6][#7]        						    nd "sp2 N of conjugated ring"
 atom [#7X2;R]=[#6][#8]        						    nd "sp2 N of conjugated ring"
 atom [#7X2;R]=[#6][#16]        						    nd "sp2 N of conjugated ring"
-atom [#7X2r5](:[#6])[#6]						    nd "N in aromatic ring due to lone pairs of size 5"
+atom [#7X2r5](:[#6])[#6]						    nb "N in aromatic ring due to lone pairs of size 5"
 atom [nX2r6](:[#6X3][NX3])([#6X3]=[O])					    nd "N in Cytosine"
 atom [nX2r5]([#6])[#8,#16]						    nc "N in aromatic ring due to lone pairs of size 5"
 atom [#7X2;R](-[#7X3]-[#6X3])=[#6X3]    				    nc "sp2 N of conjugated ring"

test/ffgaff.cpp

@@ -129,7 +129,7 @@ int ffgaff(int argc, char* argv[])
 
       // compare the calculated energy to our reference data
       energy = pFF->Energy(false);
-      if ( fabs(atof(buffer) - energy ) > 1.0e-3)
+      if (fabs(atof(buffer) - energy) > 1.0e-3)
         {
           cout << "not ok " << ++currentTest << " # calculated energy incorrect "
                << " for molecule " << mol.GetTitle() << "\n";

test/files/gaffresults.txt

@@ -1,19 +1,19 @@
-      255.83435
-      216.53914
+      1083.9238
+      -0.664855
        -7.55372
-       21.16533
+       19.1904
        74.71878
       391.26140
-      502.55043
-      281.04035
+      749.772
+      412.154
      3503.47646
-      207.16726
+      417.165
       238.58285
-      270.91856
-     1640.38665
-      255.83435
+      302.486
+     97.8035
+     1083.9238
      1288.59079
-      179.78293
-      210.78925
-      473.24610
+      292.84
+      105.406
+      391.5
        -0.55350