remarks Asn MD with GB/HCT remarks Tom Simonson, May, 2002. !-------------------------------------------------------------- ! the initial time is the ONLY parameter that has to be changed ! $inittime is set to the last time of the previous run evaluate ($inittime = 0 {ps}) evaluate ($finaltime = $inittime + 100) {100 ps equilibration} set seed = 123456 end topology @TOPPAR:topamber.inp @TOPPAR:amberpatches.pro end parameter @TOPPAR:paramber.gb.inp end segment name="ASN1" molecule name=ASN number=1 end end patch NASN refe=nil=(resid 1) end patch CASN refe=nil=(resid 1) end vector do (charge = charge + .2306) (name ht%) vector show sum (charge) (all) segment name="ASN1" molecule name=ASN number=1 end end patch NTER refe="+"=(resid 1) end patch CTER refe="-"=(resid 1) end vector show sum (charge) (all) parameter nbonds atom cdie trunc e14fac=0.8333333 ! use this to reproduce amber elec cutnb 500. ctonnb 480. ctofnb 490. ! essentially no cutoff tolerance=100. ! only build the nonbonded list once nbxmod 5 vswitch wmin=1.0 end end parameters nbonds EPS=1. WEPS=80. offset=0.09 GBHCT ! GB parameters end end ! gauche minus conformer coor ! @data/asn.-80.10.pdb REMARK CHI1=-80, CHI2=10; ENERGY = -3.92838 REMARK DATE: 3/ 6/98 14:38:33 CREATED BY USER: simonson ATOM 1 N ASN 1 26.522 -15.164 -2.651 0.00 0.00 ASN1 ATOM 2 HT1 ASN 1 25.821 -14.402 -2.738 0.00 0.00 ASN1 ATOM 3 HT2 ASN 1 26.992 -15.315 -3.566 0.00 0.00 ASN1 ATOM 4 HT3 ASN 1 27.228 -14.908 -1.932 0.00 0.00 ASN1 ATOM 5 CA ASN 1 25.834 -16.419 -2.236 0.00 0.00 ASN1 ATOM 6 HA ASN 1 25.080 -16.641 -2.979 0.00 0.00 ASN1 ATOM 7 CB ASN 1 26.844 -17.593 -2.073 0.00 0.00 ASN1 ATOM 8 HB1 ASN 1 26.370 -18.398 -1.469 0.00 0.00 ASN1 ATOM 9 HB2 ASN 1 27.757 -17.253 -1.543 0.00 0.00 ASN1 ATOM 10 CG ASN 1 27.223 -18.202 -3.434 0.00 0.00 ASN1 ATOM 11 OD1 ASN 1 26.897 -17.663 -4.497 0.00 0.00 ASN1 ATOM 12 ND2 ASN 1 27.947 -19.361 -3.377 0.00 0.00 ASN1 ATOM 13 HD21 ASN 1 28.231 -19.812 -4.222 0.00 0.00 ASN1 ATOM 14 HD22 ASN 1 28.188 -19.756 -2.491 0.00 0.00 ASN1 ATOM 15 C ASN 1 25.143 -16.177 -0.888 0.00 0.00 ASN1 ATOM 16 OT1 ASN 1 23.884 -16.213 -0.858 0.00 0.00 ASN1 ATOM 17 OT2 ASN 1 25.860 -15.961 0.127 0.00 0.00 ASN1 END write coor output=asn.-80.10.pdb end @TOPPAR:volumes.amber vector do (rmsd = rmsd * 0.9) (all) ! reduce volumes by 10% flags include gbse gbin end parameter reduce selection=(all) overwrite=true mode=average end end energy end !----------------------------- ! shake TIP3p's and ALL bonds !shake ! ncon=6000 ! reference=parameter bonds ( not resname TIP3 ) ( all ) ! tolerance=1.0e-08 !end ! weakly restrain Calpha position vector do (harmonic = 0.5) (name ca) coor disp=reference @asn.-80.10.pdb constraints harmonic end flags include harmonic end !----------------- ! Now run dynamics !------------------------------------------ ! $time is set to last time of previous run evaluate ($time = $inittime) !--------------------------------------------------------------- ! first, read "restart" files or initial coords and assign velos if ($time > 0) then coor disp=main @@$fincrd coor disp=comp @@$finvel vector do (vx = xcomp) (attribute xcomp < 999.0) vector do (vy = ycomp) (attribute xcomp < 999.0) vector do (vz = zcomp) (attribute xcomp < 999.0) vector do (vx = maxwell(250)) (attribute xcomp > 999.) vector do (vy = maxwell(250)) (attribute xcomp > 999.) vector do (vz = maxwell(250)) (attribute xcomp > 999.) else vector do (vx = maxwell(250)) (all) vector do (vy = maxwell(250)) (all) vector do (vz = maxwell(250)) (all) end if !------------------------------------- ! relax initial bad contacts if ($time = 0.) then minimize powell nstep=10 drop=10 end minimize powell nstep=10 drop=10 end end if !-------------------------- ! generate output filenames !evaluate ($traj = "output/dyn" + encode($time) + ".crd") !evaluate ($velo= "output/dyn" + encode($time) + ".vel") !evaluate ($restart ="output/dyn"+encode($time) + ".rst") !-------------- ! let it go display CPU= $CPU sec. dynamics verlet nstep=50 timest=0.001 {ps} ! 100 ps dynamics iasvel=current ! current velocities nprint=25 iprfrq=250 ! statistics output ascii=true !traj=$traj ! coord trajectory nsavc=250 vascii=true voffset=800 !velo=$velo ! velocity trajectory nsavv=10000 !save=$restart isvfrq=100000 ! restart file end stop