* Alalnine test case for QM(GAMESS)/MM * CTERM is QM and the rest is MM * Link atom is between CA and C * Runs ~ 3 min on HP-735 * stream datadir.def read rtf card * Taken from top_all22_prot.inp * 22 1 MASS 1 H 1.00800 ! polar H MASS 2 HC 1.00800 ! N-ter H MASS 3 HA 1.00800 ! nonpolar H MASS 6 HB 1.00800 ! backbone H MASS 20 C 12.01100 ! polar C MASS 22 CT1 12.01100 ! aliphatic sp3 C for CH MASS 24 CT3 12.01100 ! aliphatic sp3 C for CH3 MASS 32 CC 12.01100 ! carbonyl C for sidechains asn,asp,gln,glu MASS 54 NH1 14.00700 ! peptide nitrogen MASS 56 NH3 14.00700 ! ammonium nitrogen MASS 70 O 15.99900 ! carbonyl oxygen MASS 72 OC 15.99900 ! carboxylate oxygen mass 9 QQH 1.00800 ! link atom DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA O C BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2 ATOM OT1 OC -0.67 ! // ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT1 C OT2 ! OT1 IMPR OT1 CA OT2 C ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! / ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 end read param card * from par_all22_prot.inp * BONDS CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) qqh cc 0.0 1.0 ! Link atom ANGLES NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) qqh cc ct1 0.0 0.0 ! Link atom DIHEDRALS OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) IMPROPER OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK) NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 13.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 qqh 0.000000 0.000000 0.000000 ! Link atom end read sequ ala 1 gene mpep setup ic param ic seed mpep 1 n mpep 1 ca mpep 1 c ic build mini abnr nstep 1000 nprint 1000 addl qqh1 mpep 1 c mpep 1 ca define qm sele atom mpep 1 c .or. atom mpep 1 ot1 - .or. atom mpep 1 ot2 end ! names in quotes so they are lowercase envi input "data/ala.str" envi output "scratch/ala.gms" envi punch "scratch/test.dat" envi dictnry "scratch/test.f10" envi work15 "scratch/test.f15" envi dasort "scratch/test.f20" gamess remove sele qm end mini abnr nstep 10 nprint 10 test first tol 0.0 step 0.0005