* generate model compound B * !set identifier set id1 model_b set toppar $CHARMMDATA set top @toppar/top_all27_prot_lipid.rtf set par @toppar/par_all27_prot_lipid.prm set toppar top_mmtsb_example.str system "mkdir gauss" ! tolgrd setting: RMS force tolerance to exit minimizer set a 0.0001 ! read the topology open unit 9 read form name @top read rtf card unit 9 close unit 9 ! read the parameters open unit 9 read form name @par read para card unit 9 close unit 9 !stream toppar file with additional rtf/param information stream @toppar read sequence cards * cmpd model 1 * 1 mod1 generate a first none last none setup warn !generate preliminary IC table !ic generate !stop !build structure based on internal coordinates ic param ic seed 1 h11 1 c1 1 c2 ic build coor print !write initial coordinates open unit 26 write form name @id1_gen.pdb write coor pdb unit 26 !minimization with infinite nonbond cutoff update cutnb 99.0 ctofnb 98.0 ctonnb 97.0 switch vswitch mini abnr nstep 200 nprint 10 mini nraph nstep 50 !write minmized coordinates open unit 26 write form name @id1_min.pdb write coor pdb unit 26 !print internal coordinates based on the minimized !structure ic fill ic print !Create input file for Gaussian QM program. Includes both !energy minimization and frequency calculation. Note the !total charge is assummed to be zero open unit 30 write form name gauss/@id1_opt_freq_mp2.com prnlev 3 mmqm unit 30 %chk=@id1_opt_freq_mp2.chk %nproc=2 #MP2/6-31G* Opt pop=(mk,dipole) density=current @id1 optimized at MP2/6-31G* 0 1 END GAUSSIAN_BASIS --link1-- %nprocs=2 %chk=@id1_opt_freq_mp2.chk #MP2/6-31G* geom=allcheck freq IOP(7/33=1) @id1 frequency 0 1 END !end write gaussian input file !alter IC table to obtain the global energy minimum conformation coor init !reset all coordinates ic edit dihe 1 c1 1 c2 1 n3 1 n4 0.0 dihe 1 c2 1 n3 1 n4 1 c5 180.0 dihe 1 n3 1 n4 1 c5 1 c6 180.0 end ic seed 1 h11 1 c1 1 c2 ic build coor print open unit 26 write form name @id1_gen_2.pdb write coor pdb unit 26 update cutnb 99.0 ctofnb 98.0 ctonnb 97.0 switch vswitch mini abnr nstep 200 nprint 10 mini nraph nstep 50 open unit 26 write form name @id1_min_2.pdb write coor pdb unit 26 !print internal coordinates based on the minimized !structure ic fill ic print !Create input file for Gaussian QM program. Includes both !energy minimization and frequency calculation. Note the !total charge is assummed to be zero open unit 30 write form name gauss/@id1_opt_freq_mp2_2.com prnlev 3 mmqm unit 30 %chk=@id1_opt_freq_mp2_2.chk %nproc=2 #MP2/6-31G* Opt pop=(mk,dipole) density=current @id1 optimized at MP2/6-31G* 0 1 END GAUSSIAN_BASIS --link1-- %nprocs=2 %chk=@id1_opt_freq_mp2_2.chk #MP2/6-31G* geom=allcheck freq IOP(7/33=1) @id1 frequency 0 1 END !end write gaussian input file !alter IC table to obtain second minimum energy conformation coor init ic edit dihe 1 c1 1 c2 1 n3 1 n4 180.0 dihe 1 c2 1 n3 1 n4 1 c5 0.0 dihe 1 n3 1 n4 1 c5 1 c6 180.0 end ic seed 1 h11 1 c1 1 c2 ic build coor print open unit 26 write form name @id1_gen_3.pdb write coor pdb unit 26 update cutnb 99.0 ctofnb 98.0 ctonnb 97.0 switch vswitch mini abnr nstep 200 nprint 10 mini nraph nstep 50 open unit 26 write form name @id1_min_3.pdb write coor pdb unit 26 !print internal coordinates based on the minimized !structure ic fill ic print !Create input file for Gaussian QM program. Includes both !energy minimization and frequency calculation. Note the !total charge is assummed to be zero open unit 30 write form name gauss/@id1_opt_freq_mp2_3.com prnlev 3 mmqm unit 30 %chk=@id1_opt_freq_mp2_3.chk %nproc=2 #MP2/6-31G* Opt pop=(mk,dipole) density=current @id1 optimized at MP2/6-31G* 0 1 END GAUSSIAN_BASIS --link1-- %nprocs=2 %chk=@id1_opt_freq_mp2_3.chk #MP2/6-31G* geom=allcheck freq IOP(7/33=1) @id1 frequency 0 1 END !end write gaussian input file !alter IC table to obtain second minimum energy conformation coor init ic edit dihe 1 c1 1 c2 1 n3 1 n4 0.0 dihe 1 c2 1 n3 1 n4 1 c5 0.0 dihe 1 n3 1 n4 1 c5 1 c6 180.0 end ic seed 1 h11 1 c1 1 c2 ic build coor print open unit 26 write form name @id1_gen_4.pdb write coor pdb unit 26 update cutnb 99.0 ctofnb 98.0 ctonnb 97.0 switch vswitch mini abnr nstep 200 nprint 10 mini nraph nstep 50 open unit 26 write form name @id1_min_4.pdb write coor pdb unit 26 !print internal coordinates based on the minimized !structure ic fill ic print !Create input file for Gaussian QM program. Includes both !energy minimization and frequency calculation. Note the !total charge is assummed to be zero open unit 30 write form name gauss/@id1_opt_freq_mp2_4.com prnlev 3 mmqm unit 30 %chk=@id1_opt_freq_mp2_4.chk %nproc=2 #MP2/6-31G* Opt pop=(mk,dipole) density=current @id1 optimized at MP2/6-31G* 0 1 END GAUSSIAN_BASIS --link1-- %nprocs=2 %chk=@id1_opt_freq_mp2_4.chk #MP2/6-31G* geom=allcheck freq IOP(7/33=1) @id1 frequency 0 1 END !end write gaussian input file stop !perform surface open unit 26 write form name pacp_@id1.surf !set minimum values to offset surface to 0.0 set a ?ener set b ?elec set c ?vdw set d ?dihe set e ?angl set f ?bond set g ?urey set 1 180 if stop eq 1 then STOP label loop_pacp !CONS DIHE A 1 c23 A 1 C22 A 1 N21 A 1 H211 FORCE 10000.0 MIN 120.0 CONS DIHE A 1 c23 A 1 c22 A 1 N21 A 1 C15 FORCE 10000.0 MIN @1.0 mini abnr nstep 50 inbfrq 0 inbfrq 0 mini abnr nstep 50 inbfrq 0 inbfrq 0 mini nraph tolstp 0.000001 tolgrd 0.000001 - nstep 500 nprint 100 inbfrq 0 inbfrq 0 set 5 ?ener decr 5 by ?cdih decr 5 by @a set 6 ?elec decr 6 by @b set 7 ?vdw decr 7 by @c set 8 ?dihe decr 8 by @d set 9 ?angl decr 9 by @e set 0 ?bond decr 0 by @f set 4 ?urey decr 4 by @g calc inter = @9 + @0 + @4 write title unit 26 * @1.0 @5 @6 @7 @8 @inter * !* @1.0 @5 @6 @7 @8 @9 @0 @4 !* cons cldh ic fill ic print !open unit 26 write form name pacp.@1.pdb !write coor pdb unit 26 decr 1 by 10 if 1 ge 0 goto loop_pacp close unit 26 stop