; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Wed Oct 27 15:27:10 2010 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx4.5.1 - VERSION 4.5.1 ; ; Command line was: ; pdb2gmx4.5.1 -f initial.pdb -o vacuum.gro -ff amber96 -water None ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "amber96.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 ACE rtp ACE q 0.0 1 HC 1 ACE HH31 1 0.1123 1.008 ; qtot 0.1123 2 CT 1 ACE CH3 2 -0.3662 12.01 ; qtot -0.2539 3 HC 1 ACE HH32 3 0.1123 1.008 ; qtot -0.1416 4 HC 1 ACE HH33 4 0.1123 1.008 ; qtot -0.0293 5 C 1 ACE C 5 0.5972 12.01 ; qtot 0.5679 6 O 1 ACE O 6 -0.5679 16 ; qtot 0 ; residue 2 ALA rtp ALA q 0.0 7 N 2 ALA N 7 -0.4157 14.01 ; qtot -0.4157 8 H 2 ALA H 8 0.2719 1.008 ; qtot -0.1438 9 CT 2 ALA CA 9 0.0337 12.01 ; qtot -0.1101 10 H1 2 ALA HA 10 0.0823 1.008 ; qtot -0.0278 11 CT 2 ALA CB 11 -0.1825 12.01 ; qtot -0.2103 12 HC 2 ALA HB1 12 0.0603 1.008 ; qtot -0.15 13 HC 2 ALA HB2 13 0.0603 1.008 ; qtot -0.0897 14 HC 2 ALA HB3 14 0.0603 1.008 ; qtot -0.0294 15 C 2 ALA C 15 0.5973 12.01 ; qtot 0.5679 16 O 2 ALA O 16 -0.5679 16 ; qtot 0 ; residue 3 NME rtp NME q 0.0 17 N 3 NME N 17 -0.4157 14.01 ; qtot -0.4157 18 H 3 NME H 18 0.2719 1.008 ; qtot -0.1438 19 CT 3 NME CH3 19 -0.149 12.01 ; qtot -0.2928 20 H1 3 NME HH31 20 0.0976 1.008 ; qtot -0.1952 21 H1 3 NME HH32 21 0.0976 1.008 ; qtot -0.0976 22 H1 3 NME HH33 22 0.0976 1.008 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 2 3 1 2 4 1 2 5 1 5 6 1 5 7 1 7 8 1 7 9 1 9 10 1 9 11 1 9 15 1 11 12 1 11 13 1 11 14 1 15 16 1 15 17 1 17 18 1 17 19 1 19 20 1 19 21 1 19 22 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 6 1 1 7 1 2 8 1 2 9 1 3 6 1 3 7 1 4 6 1 4 7 1 5 10 1 5 11 1 5 15 1 6 8 1 6 9 1 7 12 1 7 13 1 7 14 1 7 16 1 7 17 1 8 10 1 8 11 1 8 15 1 9 18 1 9 19 1 10 12 1 10 13 1 10 14 1 10 16 1 10 17 1 11 16 1 11 17 1 12 15 1 13 15 1 14 15 1 15 20 1 15 21 1 15 22 1 16 18 1 16 19 1 18 20 1 18 21 1 18 22 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 1 1 2 4 1 1 2 5 1 3 2 4 1 3 2 5 1 4 2 5 1 2 5 6 1 2 5 7 1 6 5 7 1 5 7 8 1 5 7 9 1 8 7 9 1 7 9 10 1 7 9 11 1 7 9 15 1 10 9 11 1 10 9 15 1 11 9 15 1 9 11 12 1 9 11 13 1 9 11 14 1 12 11 13 1 12 11 14 1 13 11 14 1 9 15 16 1 9 15 17 1 16 15 17 1 15 17 18 1 15 17 19 1 18 17 19 1 17 19 20 1 17 19 21 1 17 19 22 1 20 19 21 1 20 19 22 1 21 19 22 1 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 5 6 9 1 2 5 7 9 3 2 5 6 9 3 2 5 7 9 4 2 5 6 9 4 2 5 7 9 2 5 7 8 9 2 5 7 9 9 6 5 7 8 9 6 5 7 9 9 5 7 9 10 9 5 7 9 11 9 5 7 9 15 9 8 7 9 10 9 8 7 9 11 9 8 7 9 15 9 7 9 11 12 9 7 9 11 13 9 7 9 11 14 9 10 9 11 12 9 10 9 11 13 9 10 9 11 14 9 15 9 11 12 9 15 9 11 13 9 15 9 11 14 9 7 9 15 16 9 7 9 15 17 9 10 9 15 16 9 10 9 15 17 9 11 9 15 16 9 11 9 15 17 9 9 15 17 18 9 9 15 17 19 9 16 15 17 18 9 16 15 17 19 9 15 17 19 20 9 15 17 19 21 9 15 17 19 22 9 18 17 19 20 9 18 17 19 21 9 18 17 19 22 9 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 2 7 5 6 4 5 9 7 8 4 9 17 15 16 4 15 19 17 18 4 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name AceAlaNme [ molecules ] ; Compound #mols Protein 1