VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Dec 28 2006 - 15:46:31 CST

Hi Matt,
as I said, all you need to do is insert bonds between monomers analogous
to those found in the existing topology file (just look at your favorite
amino acid). So, in your case (for example) you might add something like
BOND C2 +O1
and make the H23 atom be included as part of a patch (look at NTER for
an example) rather than the main residue.
If you use the modified topology file with a pdb that has several PETE
monomers with consecutive residue numbers, they will end up bonded after
you run psfgen.

Peter

wolfinbm_at_uci.edu wrote:
> Hello Peter,
> Thank you very much for your help. I already have some of what you
> described, thanks to Dr. Ritz and one of his graduate assistants (see
> attatchments). My main problem right now (I think) is getting PETE
> monomers connected together to make a polymer.
>
> Thanks and Best,
> Matt
>
>
>> Hi Matt,
>> you'll need to deal with two separate issues to get what you want:
>> 1) creating a proper topology for the PETE polymer
>> 2) getting coordinates for the membrane of interest
>>
>> Before getting started, you'll want to make sure you've read the namd
>> tutorial (including appendices) and topology file tutorials at
>> http://www.ks.uiuc.edu/Training/Tutorials/. Doing what you want to is
>> still somewhat complicated; we're currently working on things like
>> arbitrary polymer builders that will make it much easier. For now,
>> though, you'll still have to do some things by hand, which is where the
>> tutorials are useful.
>>
>> Dealing with these in order:
>> 1. Building up pretty much any polymer using VMD/psfgen is done just
>> like a polypeptide. If you look at the topology file entries for any of
>> the amino acids, you'll see that bonds are specified to -C and +N --
>> these denote bonds to the previous and next monomers in the polymer
>> chain. You need to first generate a topology file entry for your PETE
>> monomer, and then add the proper bonds to cause it to be connected in a
>> chain (and also make terminal patches, like NTER and CTER, to properly
>> cap the ends of your polymer). You can get the PETE monomer topology
>> file using a molefacture function: In the tkcon, enter
>> ::Molefacture::write_topfile pete.top $sel
>> where $sel is an atomselect object containing your PETE monomer. If your
>> version of molefacture doesn't have this let me know and I'll send you
>> the latest alpha (which also has this command present in the file menu).
>> You'll need to assign proper atom types either in molefacture or by
>> editing the topology file, and then add the bonds necessary for
>> polymerization. Armed with this topology file, feeding a pdb file
>> containing several PETE monomers to psfgen will let you build a polymer.
>>
>> Since we're talking about a pdb file with the proper coordinates, this
>> leads us neatly into
>> 2. Getting the coordinates. You'll need to generate a pdb file
>> containing the coordinates for some section of the membrane you want.
>> Since I really don't know what a PETE membrane would look like, the best
>> I can do is recommend the following steps:
>> -Write a single pete monomer as a pdb from vmd
>> -Use your favorite text editor or filter to make a pdb file with many
>> copies of it, with consecutive residue numbering
>> -Load that composite pdb into vmd, and use either the mouse or movement
>> commands to move the residues into the appropriate places for a pete
>> membrane
>> -Write the new pdb file, and then run it through psfgen to get the
>> polymer of interest
>>
>> Once you've got a single membrane layer generated, you can look at
>> making several chains with different size holes punched in them to
>> generate the different layers.
>>
>> Peter
>>
>
>
>
>
>
> ------------------------------------------------------------------------
>
> Subject:
> PET force field & topolgy files etc.
> From:
> Harindar Keer <hkeer_at_uci.edu>
> Date:
> Fri, 28 Jul 2006 17:21:25 -0700
> To:
> Thorsten Ritz <tritz_at_uci.edu>
>
> To:
> Thorsten Ritz <tritz_at_uci.edu>
>
> Content-Type:
> multipart/mixed; boundary="=-GBRiOICDGWP7dWh/5t8D"
> Message-ID:
> <1154132484.4239.14.camel_at_watson.ps.uci.edu>
> MIME-Version:
> 1.0
> X-Mailer:
> Ximian Evolution 1.4.6 (1.4.6-2)
>
>
> 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
>
>
>
>
>
> ------------------------------------------------------------------------
>
> *>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
>
> ------------------------------------------------------------------------
>
> *> 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
>
> ------------------------------------------------------------------------
>
> #############################################################
> ## 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
>
>
>
> ------------------------------------------------------------------------
>
> BIOGRF 332
> REMARK NATOM 23
> FORCEFIELD DREIDING
> FORMAT ATOM (a6,1x,i6,1x,a5,1x,a4,1x,a1,1x,i5,3f10.5,1x,a5,i3,i2,1x,f8.5,1x,f6.3,1x,f6.3,1x,i3,1x,a4)
> ATOM 1 CZ PET A 1 30.84000 -10.25200 0.00000 CZ 0 0 -0.11500 0.000 1.000 6 A
> ATOM 2 CE1 PET A 1 30.84000 -8.41200 0.00000 CE1 0 0 -0.11500 0.000 1.000 58 A
> ATOM 3 CD1 PET A 1 29.24600 -7.49200 0.00000 CD1 0 0 -0.10000 0.000 1.000 48 A
> ATOM 4 CG PET A 1 27.65300 -8.41200 0.00000 CG 0 0 -0.11500 0.000 1.000 6 A
> ATOM 5 CE2 PET A 1 29.24600 -11.17200 0.00000 CE2 0 0 -0.10000 0.000 1.000 58 A
> ATOM 6 CD2 PET A 1 27.65300 -10.25200 0.00000 CD2 0 0 -0.11500 0.000 1.000 48 A
> ATOM 7 HE1 PET A 1 31.79400 -7.86200 0.00000 HE1 0 0 0.11500 0.000 1.000 2 A
> ATOM 8 HG PET A 1 26.69900 -7.86200 0.00000 HG 0 0 0.11500 0.000 1.000 80 A
> ATOM 9 HD2 PET A 1 26.69900 -10.80300 0.00000 HD2 0 0 0.11500 0.000 1.000 1 A
> ATOM 10 HZ PET A 1 31.79400 -10.80300 0.00000 HZ 0 0 0.11500 0.000 1.000 1 A
> ATOM 11 CD3 PET A 1 29.24600 -5.65300 0.00000 CD3 0 0 0.62000 0.000 1.000 48 A
> ATOM 12 O1 PET A 1 30.84000 -4.73300 0.00000 O1 0 0 -0.76000 0.000 1.000 8 A
> ATOM 13 O2 PET A 1 27.65300 -4.73300 0.00000 O2 0 0 -0.76000 0.000 1.000 8 A
> ATOM 14 CD4 PET A 1 29.24600 -13.01200 0.00000 CD4 0 0 1.62000 0.000 1.000 48 A
> ATOM 15 O3 PET A 1 27.65300 -13.93200 0.00000 O3 0 0 -0.76000 0.000 1.000 8 A
> ATOM 16 O4 PET A 1 30.84000 -13.93200 0.00000 O4 0 0 -0.76000 0.000 1.000 8 A
> ATOM 17 C1 PET A 1 27.65300 -15.77200 0.00000 C1 0 0 -0.18000 0.000 1.000 6 A
> ATOM 18 H11 PET A 1 28.22300 -16.10100 0.93100 H11 0 0 0.09000 0.000 1.000 1 A
> ATOM 19 H12 PET A 1 28.10700 -16.03400 -1.01200 H12 0 0 0.09000 0.000 1.000 1 A
> ATOM 20 C2 PET A 1 26.06000 -16.69200 0.00000 C2 0 0 -0.27000 0.000 1.000 6 A
> ATOM 21 H21 PET A 1 25.46200 -16.41600 0.93100 H21 0 0 0.09000 0.000 1.000 1 A
> ATOM 22 H22 PET A 1 25.46200 -16.41600 -0.93100 H22 0 0 0.09000 0.000 1.000 1 A
> ATOM 23 H23 PET A 1 26.26800 -17.81300 0.00000 H23 0 0 0.09000 0.000 1.000 1 A
> FORMAT CONECT (a6,14i6)
> FORMAT ORDER (a6,i6,13f6.3)
> CONECT 1 2 5 10
> ORDER 1 1.000 1.000 1.000
> CONECT 2 1 3 7
> ORDER 2 1.000 1.000 1.000
> CONECT 3 2 4 11
> ORDER 3 1.000 1.000 1.000
> CONECT 4 3 8 6
> ORDER 4 1.000 1.000 1.000
> CONECT 5 1 6 14
> ORDER 5 1.000 1.000 1.000
> CONECT 6 4 5 9
> ORDER 6 1.000 1.000 1.000
> CONECT 7 2
> ORDER 7 1.000
> CONECT 8 4
> ORDER 8 1.000
> CONECT 9 6
> ORDER 9 1.000
> CONECT 10 1
> ORDER 10 1.000
> CONECT 11 3 12 13
> ORDER 11 1.000 1.000 1.000
> CONECT 12 11
> ORDER 12 1.000
> CONECT 13 11
> ORDER 13 1.000
> CONECT 14 5 15 16
> ORDER 14 1.000 1.000 1.000
> CONECT 15 14 17
> ORDER 15 1.000 1.000
> CONECT 16 14
> ORDER 16 1.000
> CONECT 17 15 18 19 20
> ORDER 17 1.000 1.000 1.000 1.000
> CONECT 18 17
> ORDER 18 1.000
> CONECT 19 17
> ORDER 19 1.000
> CONECT 20 17 21 22 23
> ORDER 20 1.000 1.000 1.000 1.000
> CONECT 21 20
> ORDER 21 1.000
> CONECT 22 20
> ORDER 22 1.000
> CONECT 23 20
> ORDER 23 1.000
> VDW 1
> VDW 2
> VDW 3
> VDW 4
> VDW 5
> VDW 6
> VDW 7
> VDW 8
> VDW 9
> VDW 10
> VDW 11
> VDW 12
> VDW 13
> VDW 14
> VDW 15
> VDW 16
> VDW 17
> VDW 18
> VDW 19
> VDW 20
> VDW 21
> VDW 22
> VDW 23
> LEWIS 1 -1
> LEWIS 2 3
> LEWIS 3 3
> LEWIS 4 -1
> LEWIS 5 3
> LEWIS 6 3
> LEWIS 7 1
> LEWIS 8 1
> LEWIS 9 0
> LEWIS 10 0
> LEWIS 11 3
> LEWIS 12 -1
> LEWIS 13 -1
> LEWIS 14 3
> LEWIS 15 0
> LEWIS 16 -1
> LEWIS 17 0
> LEWIS 18 0
> LEWIS 19 0
> LEWIS 20 0
> LEWIS 21 0
> LEWIS 22 0
> LEWIS 23 0
> END