Subject: PET force field & topolgy files etc. From: Harindar Keer To: Thorsten Ritz Content-Type: multipart/mixed; boundary="=-GBRiOICDGWP7dWh/5t8D" Message-Id: <1154132484.4239.14.camel@watson.ps.uci.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.6 (1.4.6-2) Date: Fri, 28 Jul 2006 17:21:25 -0700 --=-GBRiOICDGWP7dWh/5t8D Content-Type: text/plain Content-Transfer-Encoding: 7bit Dear Dr. Thorsten, Please find attached the files related to PET (polyethylene terephthalate) project With Dr. Ziwy. Fortunately, I found force field for benzoic acid in Charmm, after hint from Alex Mackerell. This enabled me to prepare force fields for the original PET molecule without any modification. Attached files are structure file: PET_psfgen.psf coordinate file: PET_psfgen.pdb topology file : PET.top parameter file: PET.par NAMD configuration file : PET.conf Also, I wanted to check with you if I can go ahead and get in touch with Joseph (MPC facility) to get cluster moved to MPC. Regards, Harindar --=-GBRiOICDGWP7dWh/5t8D Content-Disposition: attachment; filename=PET.par Content-Type: text/plain; name=PET.par; charset=UTF-8 Content-Transfer-Encoding: 7bit *>CHARMM22 All-Hydrogen Parameter File for Proteins and Lipids << *>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<< *>>>>>>>>>>>>>>>>>>>>>> July, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<< * All comments to ADM jr. via the CHARMM web site: www.charmm.org * parameter set discussion forum * BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! CAP CAP 370.000 1.3600 ! pyridines HP CAP 340.000 1.0800 ! benzene CAP CC 200.000 1.5000 ! nicotinic acid (pyridine carboxylate) OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid OC CT2x 340.0 1.43 ! phosphate lipid section !LPPC : OSL CTL2 CT2x HA2 309.00 1.111 ! alkanes, lipid section !LPPC : CTL2 HAL2 CT2x CT3x 222.500 1.528 ! alkanes, 3/92 lipid section !LPPC : CTL2 CTL3 CT3x HA3 322.00 1.111 ! alkanes, 4/98 lipid section !LPPC : CTL3 HAL3 ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types Ktheta Theta0 Kub S0 ! CAP CAP CAP 90.00 122.00 30.00 2.3880 ! pyridine HP CAP CAP 30.00 119.00 22.00 2.15250 ! pyridine CC CAP CAP 40.00 119.00 35.00 2.41620 ! nicotinic acid (pyridine carboxylate) CAP CC OC 40.00 118.00 50.00 2.3880 !! nicotinic acid (pyridine carboxylate) OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) CC OC CT2x 40.0 109.6 30.0 2.2651 ! methyl acetate ! LPPC CL OSL CTL2 OC CT2x HA2 60.0 109.5 ! phosphate ! LPPC OSL CTL2 HAL2 OC CT2x CT3x 75.700 110.10 ! acetic acid ! LPPC OSL CTL2 CTL3 HA2 CT2x CT3x 34.600 110.10 22.53 2.179 ! alkane, 4/98 !ETHANE HA2 CT2x HA2 35.500 109.00 5.40 1.80200 ! alkane, 3/92 !ETHANE HA3 CT3x CT2x 34.600 110.10 22.53 2.179 ! alkane, 4/98 !ETHANE HA3 CT3x HA3 35.500 108.40 5.40 1.80200 ! alkane, 3/92 !ETHANE DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! HP CAP CAP CAP 4.20 2 180.00 ! pyridines HP CAP CAP HP 1.90 2 180.00 ! pyridines CAP CAP CAP CAP 1.20 2 180.00 ! pyridines CC CAP CAP CAP 3.10 2 180.00 ! pyridines HP CAP CAP CC 4.20 2 180.00 ! aminopyridine OC CC CAP CAP 3.10 2 180.00 ! nicotinic acid (pyridine carboxylate) CAP CC OC CT2X 2.05 2 180.00 ! methyl acetate ! X CL OSL X ! This one would need more calculation CC OC CT2X HA2 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr ! X CTL2 OSL X CC OC CT2X CT3X 0.7 1 180.00 ! ethyl acetate, 12/92 ! CTL3 CTL2 OSL CL OC CT2X CT3X HA3 0.160 3 0.00 ! alkane, 4/98, yin and mackerell ! X CTL2 CTL3 X OC CC OC CT2X 0.965 1 180.00 ! methyl acetate ! OBL CL OSL CTL2 HA2 CT2X CT3X HA3 0.160 3 0.00 ! alkane, 4/98, yin and mackerell ! X CT2x CT3x X IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! HP X X CAP 15.00 0 0.00 ! pyridine NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CT2x 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. CT3x 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. !pyridine series LJ parametes (see toppar_pyridines.str) CAP 0.000000 -0.070000 1.992400 ! HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO ! JES 8/25/89 values from Jorgensen fit to hydration energy HA2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98 HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 END --=-GBRiOICDGWP7dWh/5t8D Content-Disposition: attachment; filename=PET_psfgen.pdb Content-Type: application/vnd.palm; name=PET_psfgen.pdb Content-Transfer-Encoding: 7bit REMARK original generated coordinate pdb file ATOM 1 CZ PET A 1 30.840 -10.252 0.000 1.00 0.00 A C ATOM 2 CE1 PET A 1 30.840 -8.412 0.000 1.00 0.00 A C ATOM 3 CD1 PET A 1 29.246 -7.492 0.000 1.00 0.00 A C ATOM 4 CG PET A 1 27.653 -8.412 0.000 1.00 0.00 A C ATOM 5 CE2 PET A 1 29.246 -11.172 0.000 1.00 0.00 A C ATOM 6 CD2 PET A 1 27.653 -10.252 0.000 1.00 0.00 A C ATOM 7 HE1 PET A 1 31.794 -7.862 0.000 1.00 0.00 A H ATOM 8 HG PET A 1 26.699 -7.862 0.000 1.00 0.00 A H ATOM 9 HD2 PET A 1 26.699 -10.803 0.000 1.00 0.00 A H ATOM 10 HZ PET A 1 31.794 -10.803 0.000 1.00 0.00 A H ATOM 11 CD3 PET A 1 29.246 -5.653 0.000 1.00 0.00 A C ATOM 12 O1 PET A 1 30.840 -4.733 0.000 1.00 0.00 A O ATOM 13 O2 PET A 1 27.653 -4.733 0.000 1.00 0.00 A O ATOM 14 CD4 PET A 1 29.246 -13.012 0.000 1.00 0.00 A C ATOM 15 O3 PET A 1 27.653 -13.932 0.000 1.00 0.00 A O ATOM 16 O4 PET A 1 30.840 -13.932 0.000 1.00 0.00 A O ATOM 17 C1 PET A 1 27.653 -15.772 0.000 1.00 0.00 A C ATOM 18 H11 PET A 1 28.223 -16.101 0.931 1.00 0.00 A H ATOM 19 H12 PET A 1 28.107 -16.034 -1.012 1.00 0.00 A H ATOM 20 C2 PET A 1 26.060 -16.692 0.000 1.00 0.00 A C ATOM 21 H21 PET A 1 25.462 -16.416 0.931 1.00 0.00 A H ATOM 22 H22 PET A 1 25.462 -16.416 -0.931 1.00 0.00 A H ATOM 23 H23 PET A 1 26.268 -17.813 0.000 1.00 0.00 A H END --=-GBRiOICDGWP7dWh/5t8D Content-Disposition: attachment; filename=PET_psfgen.psf Content-Type: application/x-font-linux-psf; name=PET_psfgen.psf Content-Transfer-Encoding: 7bit PSF 3 !NTITLE REMARKS original generated structure x-plor psf file REMARKS topology PET.top REMARKS segment A { first NONE; last NONE; auto angles dihedrals } 23 !NATOM 1 A 1 PET CZ CAP -0.115000 12.0110 0 2 A 1 PET CE1 CAP -0.115000 12.0110 0 3 A 1 PET CD1 CAP -0.100000 12.0110 0 4 A 1 PET CG CAP -0.115000 12.0110 0 5 A 1 PET CE2 CAP -0.100000 12.0110 0 6 A 1 PET CD2 CAP -0.115000 12.0110 0 7 A 1 PET HE1 HP 0.115000 1.0080 0 8 A 1 PET HG HP 0.115000 1.0080 0 9 A 1 PET HD2 HP 0.115000 1.0080 0 10 A 1 PET HZ HP 0.115000 1.0080 0 11 A 1 PET CD3 CC 0.620000 12.0110 0 12 A 1 PET O1 OC -0.760000 15.9990 0 13 A 1 PET O2 OC -0.760000 15.9990 0 14 A 1 PET CD4 CC 1.620000 12.0110 0 15 A 1 PET O3 OC -0.760000 15.9990 0 16 A 1 PET O4 OC -0.760000 15.9990 0 17 A 1 PET C1 CT2X -0.180000 12.0110 0 18 A 1 PET H11 HA2 0.090000 1.0080 0 19 A 1 PET H12 HA2 0.090000 1.0080 0 20 A 1 PET C2 CT3X -0.270000 12.0110 0 21 A 1 PET H21 HA3 0.090000 1.0080 0 22 A 1 PET H22 HA3 0.090000 1.0080 0 23 A 1 PET H23 HA3 0.090000 1.0080 0 23 !NBOND: bonds 1 2 1 5 1 10 2 3 2 7 3 4 3 11 4 8 5 6 5 14 6 4 6 9 11 12 11 13 14 15 14 16 15 17 17 18 17 19 17 20 20 21 20 22 20 23 37 !NTHETA: angles 1 5 14 1 2 7 2 3 11 2 1 10 2 1 5 3 11 13 3 11 12 3 4 8 3 4 6 3 2 7 3 2 1 4 6 9 4 6 5 4 3 11 4 3 2 5 14 16 5 14 15 5 6 9 5 1 10 6 5 14 6 5 1 6 4 8 12 11 13 14 15 17 15 17 20 15 17 19 15 17 18 15 14 16 17 20 23 17 20 22 17 20 21 18 17 20 18 17 19 19 17 20 21 20 23 21 20 22 22 20 23 46 !NPHI: dihedrals 1 5 6 4 1 5 6 9 1 5 14 15 1 5 14 16 1 2 3 4 1 2 3 11 2 3 4 6 2 3 4 8 2 3 11 12 2 3 11 13 2 1 5 6 2 1 5 14 3 4 6 5 3 4 6 9 3 2 1 5 3 2 1 10 4 6 5 14 4 3 2 7 4 3 11 12 4 3 11 13 5 14 15 17 5 6 4 8 5 1 2 7 6 5 1 10 6 5 14 15 6 5 14 16 6 4 3 11 7 2 3 11 7 2 1 10 8 4 3 11 8 4 6 9 9 6 5 14 10 1 5 14 14 15 17 18 14 15 17 19 14 15 17 20 15 17 20 21 15 17 20 22 15 17 20 23 16 14 15 17 18 17 20 21 18 17 20 22 18 17 20 23 19 17 20 21 19 17 20 22 19 17 20 23 0 !NIMPHI: impropers 0 !NDON: donors 0 !NACC: acceptors 0 !NNB 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 !NGRP 0 0 0 --=-GBRiOICDGWP7dWh/5t8D Content-Disposition: attachment; filename=PET.top Content-Type: text/plain; name=PET.top; charset=UTF-8 Content-Transfer-Encoding: 7bit *> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids << *>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<< *>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<< * All comments to ADM jr. via the CHARMM web site: www.charmm.org * parameter set discussion forum * 31 1 MASS 1 HP 1.00800 H ! aromatic H MASS 2 HA2 1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 3 HA3 1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 4 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 MASS 5 CT2x 12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 6 CT3x 12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 7 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 8 OC 15.99900 O ! carboxylate oxygen AUTO ANGLES DIHE ! PET is divided into two fragments(groups) benzoic acid and ester H-CO-O-CH2-CH3 and then fragements will be combined. RESI PET -1.00 ! Polyethylene terephthalate, anion GROUP ATOM CZ CAP -0.115 ! ATOM CE1 CAP -0.115 ! ATOM CD1 CAP -0.100 ! ATOM CG CAP -0.115 ! ATOM CE2 CAP -0.100 ! ATOM CD2 CAP -0.115 ! ATOM HE1 HP 0.115 ! ATOM HG HP 0.115 ! ATOM HD2 HP 0.115 ! ATOM HZ HP 0.115 ! ATOM CD3 CC 0.620 ! ATOM O1 OC -0.760 ! ATOM O2 OC -0.760 ! GROUP ATOM CD4 CC 1.620 ! chnaged the charge of CC here from 0.62 to 1.62 (1.52 b/c of OCs + 0.1 of CE2) ## ATOM O3 OC -0.760 ! ATOM O4 OC -0.760 ! ATOM C1 CT2x -0.18 ATOM H11 HA2 0.09 ATOM H12 HA2 0.09 ATOM C2 CT3x -0.27 ATOM H21 HA3 0.09 ATOM H22 HA3 0.09 ATOM H23 HA3 0.09 BOND CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 BOND CG HG CD1 CD3 CD3 O1 BOND CD2 HD2 CE1 HE1 BOND CZ HZ BOND CE2 CD4 CD4 O3 O3 C1 BOND C1 H11 C1 H12 C1 C2 BOND C2 H21 C2 H22 C2 H23 DOUB CD3 O2 CD4 O4 --=-GBRiOICDGWP7dWh/5t8D Content-Disposition: attachment; filename=PET.conf Content-Type: text/plain; name=PET.conf; charset=UTF-8 Content-Transfer-Encoding: 7bit ############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization of Chloroform box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure PET_psfgen.psf coordinates PET_psfgen.pdb if {1} { set inputname pet_molecule binCoordinates $inputname.restart.coor #inVelocities $inputname.restart.vel extendedSystem $inputname.restart.xsc } set outputname pet_molecule_eqb set temp 300 firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters par_PET_molecule.inp #specifies Force field temperature $temp # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 1.0 ;# 1fs/step rigidBonds all ;# all needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control #langevin on ;# do langevin dynamics #langevinDamping 5 ;# damping coefficient (gamma) of 5/ps #langevinTemp 410 #langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions # PME (for full-system periodic electrostatics) # Constant Pressure Control (variable volume) #useGroupPressure yes ;# needed for rigidBonds #useFlexibleCell no #useConstantArea no #langevinPiston on #langevinPistonTarget 1.01325 ;# in bar -> 1 atm #langevinPistonPeriod 100. #langevinPistonDecay 50. #langevinPistonTemp 300 # Output outputName $outputname restartfreq 5 ;# 500 steps = every 1ps dcdfreq 5 xstFreq 5 outputEnergies 1 outputPressure 1 ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # equilibration run 1000 --=-GBRiOICDGWP7dWh/5t8D--