[gmx-users] lipid itp problem
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 7 14:06:14 CEST 2008
Please make sure to include the gmx-users list on correspondence;
someone else may have a useful idea.
It looks to me that your "input.pdb" is badly broken. Is this what
PRODRG generated? Are you using this structure for anything? Where are
the coordinates for your lipid bilayer coming from?
I would suggest starting over with the minimization - take the .pdb file
that PRODRG generates (united-atom representation, as you've tried to
use here), center it in a large box to avoid PBC effects (using editconf
-c), and try again.
Just a general thought as well - it has long been said over this list
that ffgmx should not be used for any new production simulations. It is
deprecated and the results from it may not be as reliable as one of the
newer, Gromos96 force fields. I would suggest using the PRODRG beta
server to generate parameters under Gromos96 43a1. None of this is
likely the root cause of your problem, however.
-Justin
serdar durdagi wrote:
>
> Hi Justin,
>
>
>
> Thanks for your interest.
>
>
>
> Yes, I tried your suggestion. But no success. I used a single DPPC
> molecule but I got same error message:
>
>
>
> 1-4 interaction is large.
>
>
>
> When I checked, the gro file in VMD I didn't see the broken bonds
> but, very strange molecule. I attached the input pdb file and genrated
> gro file below, you can see how molecule seem now.
>
>
>
> I used below top file and mdp file.
>
>
>
> Thanks
>
>
>
> Serdar
>
>
>
>
>
>
>
> ; File 'tat_last.top' was generated
>
> ; By user: durdagis (1004)
>
> ; On host: node25
>
> ; At date: Fri Dec 14 23:32:17 2007
>
> ;
>
> ; This is your topology file
>
> ; GROningen MAchine for Chemical Simulation
>
> ;
>
> ; Include forcefield parameters
>
> #include "ffgmx.itp"
>
> #include "lipid_july3.itp"
>
>
>
>
>
> #ifdef FLEX_SPC
>
> #include "flexspc.itp"
>
> #else
>
> #include "spc.itp"
>
> #endif
>
>
>
> ; Include Position restraint file
>
> #ifdef POSRES
>
> #include "posre.itp"
>
> #endif
>
>
>
> #ifdef POSRES_WATER
>
> ; Position restraint for each water oxygen
>
> [ position_restraints ]
>
> ; i funct fcx fcy fcz
>
> 1 1 1000 1000 1000
>
> #endif
>
> ; Include generic topology for ions
>
> #include "ions.itp"
>
> [ system ]
>
> ; Name
>
> GROningen MAchine for Chemical Simulation in water
>
> [ molecules ]
>
> ; Compound #mols
>
> MOL 1
>
>
>
>
>
>
>
> title = vals
>
> cpp = /usr/bin/cpp
>
> define = -DFLEXIBLE
>
> constraints = none
>
> integrator = steep
>
> dt = 0.002 ; ps !
>
> nsteps = 500
>
> nstlists = 10
>
> ns_type = grid
>
> rlist = 1.0
>
> coulombtype = PME
>
> rcoulomb = 1.0
>
> vdwtype = cut-off
>
> rvdw = 1.0
>
> fourierspacing = 0.12
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft = yes
>
> ;
>
> ; Energy minimizing stuff
>
> ;
>
> emtol = 100.0
>
> emsteps = 0.01
>
>
>
>
>
>
>
> input pdb file:
>
>
>
> HETATM 3585 N1 MOL 344 94.416 32.830 63.679 1.00 0.00
>
> HETATM 3586 C7 MOL 344 95.542 33.836 63.720 1.00 0.00
>
> HETATM 3587 C6 MOL 344 94.989 31.468 63.356 1.00 0.00
>
> HETATM 3588 C5 MOL 344 93.768 32.781 65.051 1.00 0.00
>
> HETATM 3589 C2 MOL 344 93.451 33.264 62.576 1.00 0.00
>
> HETATM 3590 C3 MOL 344 92.000 32.755 62.728 1.00 0.00
>
> HETATM 3591 O4 MOL 344 91.364 33.488 63.800 1.00 0.00
>
> HETATM 3592 P8 MOL 344 89.854 33.162 64.131 1.00 0.00
>
> HETATM 3593 O9 MOL 344 89.306 32.120 63.240 1.00 0.00
>
> HETATM 3594 O11 MOL 344 89.264 34.596 63.790 1.00 0.00
>
> HETATM 3595 C12 MOL 344 88.633 35.296 64.886 1.00 0.00
>
> HETATM 3596 C13 MOL 344 87.859 36.555 64.438 1.00 0.00
>
> HETATM 3597 O31 MOL 344 86.457 36.247 64.167 1.00 0.00
>
> HETATM 3598 C32 MOL 344 86.039 35.477 63.137 1.00 0.00
>
> HETATM 3599 O46 MOL 344 86.766 34.966 62.307 1.00 0.00
>
> HETATM 3600 C33 MOL 344 84.528 35.376 63.109 1.00 0.00
>
> HETATM 3601 C34 MOL 344 83.940 35.708 61.716 1.00 0.00
>
> HETATM 3602 C35 MOL 344 82.418 35.958 61.783 1.00 0.00
>
> HETATM 3603 C36 MOL 344 81.838 36.253 60.381 1.00 0.00
>
> HETATM 3604 C37 MOL 344 80.336 36.603 60.468 1.00 0.00
>
> HETATM 3605 C38 MOL 344 79.673 36.656 59.075 1.00 0.00
>
> HETATM 3606 C39 MOL 344 78.174 37.009 59.194 1.00 0.00
>
> HETATM 3607 C40 MOL 344 77.419 36.727 57.879 1.00 0.00
>
> HETATM 3608 C41 MOL 344 75.928 37.109 57.997 1.00 0.00
>
> HETATM 3609 C42 MOL 344 75.135 36.657 56.753 1.00 0.00
>
> HETATM 3610 C43 MOL 344 73.649 37.059 56.861 1.00 0.00
>
> HETATM 3611 C44 MOL 344 72.848 36.575 55.632 1.00 0.00
>
> HETATM 3612 C45 MOL 344 71.364 36.979 55.741 1.00 0.00
>
> HETATM 3613 C1 MOL 344 70.565 36.525 54.503 1.00 0.00
>
> HETATM 3614 C8 MOL 344 69.084 36.930 54.621 1.00 0.00
>
> HETATM 3615 C14 MOL 344 88.557 37.342 63.302 1.00 0.00
>
> HETATM 3616 O15 MOL 344 88.039 38.699 63.252 1.00 0.00
>
> HETATM 3617 C16 MOL 344 86.851 38.927 62.660 1.00 0.00
>
> HETATM 3618 O30 MOL 344 86.302 38.141 61.922 1.00 0.00
>
> HETATM 3619 C17 MOL 344 86.266 40.258 63.045 1.00 0.00
>
> HETATM 3620 C18 MOL 344 84.723 40.254 63.110 1.00 0.00
>
> HETATM 3621 C19 MOL 344 84.039 40.408 61.734 1.00 0.00
>
> HETATM 3622 C20 MOL 344 82.514 40.540 61.923 1.00 0.00
>
> HETATM 3623 C21 MOL 344 81.763 40.697 60.586 1.00 0.00
>
> HETATM 3624 C22 MOL 344 80.259 40.925 60.844 1.00 0.00
>
> HETATM 3625 C23 MOL 344 79.458 41.046 59.533 1.00 0.00
>
> HETATM 3626 C24 MOL 344 77.956 41.233 59.823 1.00 0.00
>
> HETATM 3627 C25 MOL 344 77.135 41.312 58.520 1.00 0.00
>
> HETATM 3628 C26 MOL 344 75.624 41.381 58.820 1.00 0.00
>
> HETATM 3629 C27 MOL 344 74.797 41.453 57.521 1.00 0.00
>
> HETATM 3630 C28 MOL 344 73.287 41.435 57.829 1.00 0.00
>
> HETATM 3631 C29 MOL 344 72.450 41.551 56.539 1.00 0.00
>
> HETATM 3632 C9 MOL 344 70.941 41.512 56.854 1.00 0.00
>
> HETATM 3633 C10 MOL 344 70.101 41.752 55.588 1.00 0.00
>
> HETATM 3634 O10 MOL 344 89.674 32.756 65.547 1.00 0.00
>
> END
>
>
>
>
>
>
>
> generated gro file:
>
>
>
> GROningen MAchine for Chemical Simulation in water
>
> 50
>
> 1MOL C31 1 3.445 1.823 2.546
>
> 1MOL C30 2 3.557 1.924 2.550
>
> 1MOL C29 3 3.502 1.687 2.514
>
> 1MOL C28 4 3.379 1.818 2.683
>
> 1MOL C27 5 3.347 1.867 2.435
>
> 1MOL C26 6 3.203 1.816 2.451
>
> 1MOL C25 7 3.139 1.889 2.558
>
> 1MOL C24 8 2.988 1.856 2.591
>
> 1MOL C23 9 2.933 1.752 2.502
>
> 1MOL C22 10 2.929 2.000 2.557
>
> 1MOL C21 11 2.866 2.070 2.667
>
> 1MOL C20 12 2.788 2.195 2.622
>
> 1MOL C19 13 2.648 2.165 2.595
>
> 1MOL C18 14 2.607 2.088 2.492
>
> 1MOL C17 15 2.679 2.037 2.409
>
> 1MOL C15 16 2.456 2.078 2.489
>
> 1MOL O16 17 2.397 2.111 2.350
>
> 1MOL O14 18 2.245 2.136 2.356
>
> 1MOL C13 19 2.187 2.166 2.216
>
> 1MOL C12 20 2.036 2.201 2.225
>
> 1MOL O11 21 1.970 2.206 2.086
>
> 1MOL P8 22 1.820 2.241 2.097
>
> 1MOL O9 23 1.745 2.213 1.966
>
> 1MOL O10 24 1.596 2.251 1.978
>
> 1MOL O7 25 1.516 2.206 1.853
>
> 1MOL C6 26 1.368 2.246 1.864
>
> 1MOL C5 27 1.288 2.198 1.741
>
> 1MOL N4 28 1.139 2.238 1.752
>
> 1MOL C2 29 1.059 2.193 1.628
>
> 1MOL C3 30 0.911 2.233 1.640
>
> 1MOL C1 31 2.859 2.273 2.508
>
> 1MOL C32 32 2.806 2.412 2.503
>
> 1MOL O33 33 2.688 2.433 2.444
>
> 1MOL C34 34 2.633 2.354 2.370
>
> 1MOL O35 35 2.629 2.566 2.483
>
> 1MOL C36 36 2.475 2.566 2.489
>
> 1MOL C37 37 2.407 2.581 2.352
>
> 1MOL C38 38 2.254 2.594 2.370
>
> 1MOL C39 39 2.179 2.610 2.237
>
> 1MOL C40 40 2.029 2.633 2.262
>
> 1MOL C41 41 1.949 2.645 2.131
>
> 1MOL C42 42 1.798 2.664 2.160
>
> 1MOL C43 43 1.716 2.671 2.030
>
> 1MOL C44 44 1.565 2.678 2.060
>
> 1MOL C45 45 1.482 2.686 1.930
>
> 1MOL C46 46 1.332 2.684 1.961
>
> 1MOL C47 47 1.248 2.695 1.832
>
> 1MOL C48 48 1.097 2.692 1.864
>
> 1MOL C49 49 1.013 2.715 1.737
>
> 1MOL C50 50 2.970 1.816 2.733
>
> 4.51490 4.51490 4.51490
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --- Justin A. Lemkul /<jalemkul at vt.edu>/ schrieb am *Mo, 7.7.2008:
> *
>
> *Von: Justin A. Lemkul <jalemkul at vt.edu>
> Betreff: Re: [gmx-users] lipid itp problem
> An: durdagis at yahoo.de, "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Datum: Montag, 7. Juli 2008, 13:08
>
> *
>
> *"Broken bonds" are probably a visualization artefact. Did you try
> what
> I suggested about minimizing just DPPC? Better yet, try minimizing one
> single DPPC molecule in vacuo to see if that succeeds, then move up to
> the bilayer, etc.
>
> Also, increasing the table-extension is usually not going to solve
> anything. If you're system is exploding, it's going to explode no
> matter what the table-extension is.
>
> -Justin
>
> serdar durdagi wrote:
> >
> > Dear all,
> >
> >
> >
> > Sorry for the previous e-mail format. I am writing again the problem.
> >
> >
> >
> > I am trying to simulate drug at the binding site of the receptor
> > surrounded by DPPC bilayer system. I have problem at the energy
> > minimisation step. Always, I am getting below error message:
> >
> >
> >
> > Warning: 1-4 interaction between 3642 and 3647 at distance 1.325 which
> > is larger than the 1-4 table size 1.000 nm These are ignored for the
> > rest of the simulation This usually means your system is exploding, if
> > not, you should increase table-extension in your mdp file
> >
> >
> >
> > Step= 0, Dmax= 1.0e-02 nm, Epot= 7.16584e+15 Fmax= 5.29841e+18, atom=
> > 2662 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.19114e+12 Fmax= 2.10320e+14,
> > atom= 3605 Step= 2, Dmax= 1.2e-02 nm, Epot= 1.39843e+10 Fmax=
> > 8.84756e+11, atom= 2662 Step= 3, Dmax= 1.4e-02 nm, Epot= 1.36040e+09
> > Fmax= 5.31692e+10, atom= 2661
> >
> >
> >
> >
> >
> > When I try to increase table-extension to more than 1.0, 1-4
> > interaction always increases.
> >
> >
> >
> > I checked the *.gro file, it seems during the minimisation, bonds at
> > protein and drg molecules are fine however, bonds at the DPPC
> > molecules are broken.
> >
> >
> >
> > I guess problem is at the *.itp file of dppc. I produced *.itp file of
> > DPPC from PRODRG. *itp file of lipid and *.mdp file for energy
> > minimisation are attached below. Could any body give a clue for the
> > solution? Many thanks in advanced.
> >
> >
> >
> > Serdar Durdagi
> >
> >
> >
> >
> > ;
> >
> > ;
> >
> > ; This file was generated by PRODRG version 071121.0636
> >
> > ; PRODRG written/copyrighted by Daan van Aalten
> >
> > ; and Alexander Schuettelkopf
> >
> > ;
> >
> > ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> >
> > ;
> >
> > ; When using this software in a publication, cite:
> >
> > ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> >
> > ; PRODRG - a tool for high-throughput crystallography
> >
> > ; of protein-ligand complexes.
> >
> > ; Acta Crystallogr. D60, 1355--1363.
> >
> > ;
> >
> > ;
> >
> > [ moleculetype ]
> >
> > ; Name nrexcl
> >
> > MOL 3
> >
> > [ atoms ]
> >
> > ; nr type resnr resid atom cgnr charge mass
> >
> > 1 CH3 1 MOL C8 1 -0.033 15.0350
> >
> > 2 CH2 1 MOL C1 1 0.008 14.0270
> >
> > 3 CH2 1 MOL C45 1 0.008 14.0270
> >
> > 4 CH2 1 MOL C44 1 0.009 14.0270
> >
> > 5 CH2 1 MOL C43 1 0.008 14.0270
> >
> > 6 CH2 1 MOL C42 2 0.000 14.0270
> >
> > 7 CH2 1 MOL C41 2 0.000 14.0270
> >
> > 8 CH2 1 MOL C40 3 0.000 14.0270
> >
> > 9 CH2 1 MOL C39 3 0.000 14.0270
> >
> > 10 CH2 1 MOL C38 4 0.000 14.0270
> >
> > 11 CH2 1 MOL C37 4 0.000 14.0270
> >
> > 12 CH2 1 MOL C36 5 0.000 14.0270
> >
> > 13 CH2 1 MOL C35 5 0.000 14.0270
> >
> > 14 CH2 1 MOL C34 6 0.000 14.0270
> >
> > 15 CH2 1 MOL C33 7 0.036 14.0270
> >
> > 16 C 1 MOL C32 7 0.438 12.0110
> >
> > 17 O 1 MOL O46 7 -0.551 15.9994
> >
> > 18 OS 1 MOL O31 7 -0.160 15.9994
> >
> > 19 CS1 1 MOL C13 7 0.237 13.0190
> >
> > 20 CH2 1 MOL C12 8 0.000 14.0270
> >
> > 21 OS 1 MOL O11 9 -0.256 15.9994
> >
> > 22 P 1 MOL P8 9 0.998 30.9738
> >
> > 23 OM 1 MOL O10 9 -0.743 15.9994
> >
> > 24 OM 1 MOL O9 9 -0.743 15.9994
> >
> > 25 OS 1 MOL O4 9 -0.256 15.9994
> >
> > 26 CH2 1 MOL C3 10 0.041 14.0270
> >
> > 27 CH2 1 MOL C2 10 0.041 14.0270
> >
> > 28 NL 1 MOL N1 10 0.918 14.0067
> >
> > 29 CH3 1 MOL C6 11 0.000 15.0350
> >
> > 30 CH3 1 MOL C5 11 0.000 15.0350
> >
> > 31 CH3 1 MOL C7 12 0.000 15.0350
> >
> > 32 CS2 1 MOL C14 13 0.242 14.0270
> >
> > 33 OS 1 MOL O15 13 -0.162 15.9994
> >
> > 34 C 1 MOL C16 13 0.437 12.0110
> >
> > 35 O 1 MOL O30 13 -0.553 15.9994
> >
> > 36 CH2 1 MOL C17 13 0.036 14.0270
> >
> > 37 CH2 1 MOL C18 14 0.000 14.0270
> >
> > 38 CH2 1 MOL C19 14 0.000 14.0270
> >
> > 39 CH2 1 MOL C20 15 0.000 14.0270
> >
> > 40 CH2 1 MOL C21 15 0.000 14.0270
> >
> > 41 CH2 1 MOL C22 16 0.000 14.0270
> >
> > 42 CH2 1 MOL C23 16 0.000 14.0270
> >
> > 43 CH2 1 MOL C24 17 0.000 14.0270
> >
> > 44 CH2 1 MOL C25 17 0.000 14.0270
> >
> > 45 CH2 1 MOL C26 18 0.000 14.0270
> >
> > 46 CH2 1 MOL C27 19 0.008 14.0270
> >
> > 47 CH2 1 MOL C28 19 0.008 14.0270
> >
> > 48 CH2 1 MOL C29 19 0.008 14.0270
> >
> > 49 CH2 1 MOL C9 19 0.009 14.0270
> >
> > 50 CH3 1 MOL C10 19 -0.033 15.0350
> >
> > [ bonds ]
> >
> > ; ai aj fu c0, c1, ...
> >
> > 1 2 1 0.153 334720.0 0.153 334720.0 ; C8 C1
> >
> > 2 3 1 0.153 334720.0 0.153 334720.0 ; C1 C45
> >
> > 3 4 1 0.153 334720.0 0.153 334720.0 ; C45 C44
> >
> > 4 5 1 0.153 334720.0 0.153 334720.0 ; C44 C43
> >
> > 5 6 1 0.153 334720.0 0.153 334720.0 ; C43 C42
> >
> > 6 7 1 0.153 334720.0 0.153 334720.0 ; C42 C41
> >
> > 7 8 1 0.153 334720.0 0.153 334720.0 ; C41 C40
> >
> > 8 9 1 0.153 334720.0 0.153 334720.0 ; C40 C39
> >
> > 9 10 1 0.153 334720.0 0.153 334720.0 ; C39 C38
> >
> > 10 11 1 0.153 334720.0 0.153 334720.0 ; C38 C37
> >
> > 11 12 1 0.153 334720.0 0.153 334720.0 ; C37 C36
> >
> > 12 13 1 0.153 334720.0 0.153 334720.0 ; C36 C35
> >
> > 13 14 1 0.153 334720.0 0.153 334720.0 ; C35 C34
> >
> > 14 15 1 0.153 334720.0 0.153 334720.0 ; C34 C33
> >
> > 15 16 1 0.153 334720.0 0.153 334720.0 ; C33 C32
> >
> > 16 17 1 0.123 502080.0 0.123 502080.0 ; C32 O46
> >
> > 16 18 1 0.136 376560.0 0.136 376560.0 ; C32 O31
> >
> > 18 19 1 0.144 251040.0 0.144 251040.0 ; O31 C13
> >
> > 19 20 1 0.153 251040.0 0.153 251040.0 ; C13 C12
> >
> > 19 32 1 0.152 251040.0 0.152 251040.0 ; C13 C14
> >
> > 20 21 1 0.143 251040.0 0.143 251040.0 ; C12 O11
> >
> > 21 22 1 0.161 251040.0 0.161 251040.0 ; O11 P8
> >
> > 22 23 1 0.148 376560.0 0.148 376560.0 ; P8 O10
> >
> > 22 24 1 0.148 376560.0 0.148 376560.0 ; P8 O9
> >
> > 22 25 1 0.161 251040.0 0.161 251040.0 ; P8 O4
> >
> > 25 26 1 0.143 251040.0 0.143 251040.0 ; O4 C3
> >
> > 26 27 1 0.153 334720.0 0.153 334720.0 ; C3 C2
> >
> > 27 28 1 0.147 376560.0 0.147 376560.0 ; C2 N1
> >
> > 28 29 1 0.147 376560.0 0.147 376560.0 ; N1 C6
> >
> > 28 30 1 0.147 376560.0 0.147 376560.0 ; N1 C5
> >
> > 28 31 1 0.147 376560.0 0.147 376560.0 ; N1 C7
> >
> > 32 33 1 0.144 251040.0 0.144 251040.0 ; C14 O15
> >
> > 33 34 1 0.136 376560.0 0.136 376560.0 ; O15 C16
> >
> > 34 35 1 0.123 502080.0 0.123 502080.0 ; C16 O30
> >
> > 34 36 1 0.153 334720.0 0.153 334720.0 ; C16 C17
> >
> > 36 37 1 0.153 334720.0 0.153 334720.0 ; C17 C18
> >
> > 37 38 1 0.153 334720.0 0.153 334720.0 ; C18 C19
> >
> > 38 39 1 0.153 334720.0 0.153 334720.0 ; C19 C20
> >
> > 39 40 1 0.153 334720.0 0.153 334720.0 ; C20 C21
> >
> > 40 41 1 0.153 334720.0 0.153 334720.0 ; C21 C22
> >
> > 41 42 1 0.153 334720.0 0.153 334720.0 ; C22 C23
> >
> > 42 43 1 0.153 334720.0 0.153 334720.0 ; C23 C24
> >
> > 43 44 1 0.153 334720.0 0.153 334720.0 ; C24 C25
> >
> > 44 45 1 0.153 334720.0 0.153 334720.0 ; C25 C26
> >
> > 45 46 1 0.153 334720.0 0.153 334720.0 ; C26 C27
> >
> > 46 47 1 0.153 334720.0 0.153 334720.0 ; C27 C28
> >
> > 47 48 1 0.153 334720.0 0.153 334720.0 ; C28 C29
> >
> > 48 49 1 0.153 334720.0 0.153 334720.0 ; C29 C9
> >
> > 49 50 1 0.153 334720.0 0.153 334720.0 ; C9 C10
> >
> > [ pairs ]
> >
> > ; ai aj fu c0, c1, ...
> >
> > 1 4 1 ; C8 C44
> >
> > 2 5 1 ; C1 C43
> >
> > 3 6 1 ; C45 C42
> >
> > 4 7 1 ; C44 C41
> >
> > 5 8 1 ; C43 C40
> >
> > 6 9 1 ; C42 C39
> >
> > 7 10 1 ; C41 C38
> >
> > 8 11 1 ; C40 C37
> >
> > 9 12 1 ; C39 C36
> >
> > 10 13 1 ; C38 C35
> >
> > 11 14 1 ; C37 C34
> >
> > 12 15 1 ; C36 C33
> >
> > 13 16 1 ; C35 C32
> >
> > 14 17 1 ; C34 O46
> >
> > 14 18 1 ; C34 O31
> >
> > 15 19 1 ; C33 C13
> >
> > 16 20 1 ; C32 C12
> >
> > 16 32 1 ; C32 C14
> >
> > 17 19 1 ; O46 C13
> >
> > 18 21 1 ; O31 O11
> >
> > 18 33 1 ; O31 O15
> >
> > 19 22 1 ; C13 P8
> >
> > 19 34 1 ; C13 C16
> >
> > 20 23 1 ; C12 O10
> >
> > 20 24 1 ; C12 O9
> >
> > 20 25 1 ; C12 O4
> >
> > 20 33 1 ; C12 O15
> >
> > 21 26 1 ; O11 C3
> >
> > 21 32 1 ; O11 C14
> >
> > 22 27 1 ; P8 C2
> >
> > 23 26 1 ; O10 C3
> >
> > 24 26 1 ; O9 C3
> >
> > 25 28 1 ; O4 N1
> >
> > 26 29 1 ; C3 C6
> >
> > 26 30 1 ; C3 C5
> >
> > 26 31 1 ; C3 C7
> >
> > 32 35 1 ; C14 O30
> >
> > 32 36 1 ; C14 C17
> >
> > 33 37 1 ; O15 C18
> >
> > 34 38 1 ; C16 C19
> >
> > 35 37 1 ; O30 C18
> >
> > 36 39 1 ; C17 C20
> >
> > 37 40 1 ; C18 C21
> >
> > 38 41 1 ; C19 C22
> >
> > 39 42 1 ; C20 C23
> >
> > 40 43 1 ; C21 C24
> >
> > 41 44 1 ; C22 C25
> >
> > 42 45 1 ; C23 C26
> >
> > 43 46 1 ; C24 C27
> >
> > 44 47 1 ; C25 C28
> >
> > 45 48 1 ; C26 C29
> >
> > 46 49 1 ; C27 C9
> >
> > 47 50 1 ; C28 C10
> >
> > [ angles ]
> >
> > ; ai aj ak fu c0, c1, ...
> >
> > 1 2 3 1 111.0 460.2 111.0 460.2 ; C8 C1 C45
> >
> > 2 3 4 1 111.0 460.2 111.0 460.2 ; C1 C45 C44
> >
> > 3 4 5 1 111.0 460.2 111.0 460.2 ; C45 C44 C43
> >
> > 4 5 6 1 111.0 460.2 111.0 460.2 ; C44 C43 C42
> >
> > 5 6 7 1 111.0 460.2 111.0 460.2 ; C43 C42 C41
> >
> > 6 7 8 1 111.0 460.2 111.0 460.2 ; C42 C41 C40
> >
> > 7 8 9 1 111.0 460.2 111.0 460.2 ; C41 C40 C39
> >
> > 8 9 10 1 111.0 460.2 111.0 460.2 ; C40 C39 C38
> >
> > 9 10 11 1 111.0 460.2 111.0 460.2 ; C39 C38 C37
> >
> > 10 11 12 1 111.0 460.2 111.0 460.2 ; C38 C37 C36
> >
> > 11 12 13 1 111.0 460.2 111.0 460.2 ; C37 C36 C35
> >
> > 12 13 14 1 111.0 460.2 111.0 460.2 ; C36 C35 C34
> >
> > 13 14 15 1 111.0 460.2 111.0 460.2 ; C35 C34 C33
> >
> > 14 15 16 1 111.0 460.2 111.0 460.2 ; C34 C33 C32
> >
> > 15 16 17 1 121.0 502.1 121.0 502.1 ; C33 C32 O46
> >
> > 15 16 18 1 120.0 418.4 120.0 418.4 ; C33 C32 O31
> >
> > 17 16 18 1 120.0 418.4 120.0 418.4 ; O46 C32 O31
> >
> > 16 18 19 1 109.5 334.7 109.5 334.7 ; C32 O31 C13
> >
> > 18 19 20 1 109.5 284.5 109.5 284.5 ; O31 C13 C12
> >
> > 18 19 32 1 109.5 284.5 109.5 284.5 ; O31 C13 C14
> >
> > 20 19 32 1 109.5 251.0 109.5 251.0 ; C12 C13 C14
> >
> > 19 20 21 1 111.0 460.2 111.0 460.2 ; C13 C12 O11
> >
> > 20 21 22 1 120.0 397.5 120.0 397.5 ; C12 O11 P8
> >
> > 21 22 23 1 109.6 397.5 109.6 397.5 ; O11 P8 O10
> >
> > 21 22 24 1 109.6 397.5 109.6 397.5 ; O11 P8 O9
> >
> > 21 22 25 1 103.0 397.5 103.0 397.5 ; O11 P8 O4
> >
> > 23 22 24 1 120.0 585.8 120.0 585.8 ; O10 P8 O9
> >
> > 23 22 25 1 109.6 397.5 109.6 397.5 ; O10 P8 O4
> >
> > 24 22 25 1 109.6 397.5 109.6 397.5 ; O9 P8 O4
> >
> > 22 25 26 1 120.0 397.5 120.0 397.5 ; P8 O4 C3
> >
> > 25 26 27 1 109.5 460.2 109.5 460.2 ; O4 C3 C2
> >
> > 26 27 28 1 109.5 460.2 109.5 460.2 ; C3 C2 N1
> >
> > 27 28 29 1 109.5 376.6 109.5 376.6 ; C2 N1 C6
> >
> > 27 28 30 1 109.5 376.6 109.5 376.6 ; C2 N1 C5
> >
> > 27 28 31 1 109.5 376.6 109.5 376.6 ; C2 N1 C7
> >
> > 29 28 30 1 109.5 376.6 109.5 376.6 ; C6 N1 C5
> >
> > 29 28 31 1 109.5 376.6 109.5 376.6 ; C6 N1 C7
> >
> > 30 28 31 1 109.5 376.6 109.5 376.6 ; C5 N1 C7
> >
> > 19 32 33 1 109.5 284.5 109.5 284.5 ; C13 C14 O15
> >
> > 32 33 34 1 109.5 334.7 109.5 334.7 ; C14 O15 C16
> >
> > 33 34 35 1 120.0 418.4 120.0 418.4 ; O15 C16 O30
> >
> > 33 34 36 1 120.0 418.4 120.0 418.4 ; O15 C16 C17
> >
> > 35 34 36 1 121.0 502.1 121.0 502.1 ; O30 C16 C17
> >
> > 34 36 37 1 111.0 460.2 111.0 460.2 ; C16 C17 C18
> >
> > 36 37 38 1 111.0 460.2 111.0 460.2 ; C17 C18 C19
> >
> > 37 38 39 1 111.0 460.2 111.0 460.2 ; C18 C19 C20
> >
> > 38 39 40 1 111.0 460.2 111.0 460.2 ; C19 C20 C21
> >
> > 39 40 41 1 111.0 460.2 111.0 460.2 ; C20 C21 C22
> >
> > 40 41 42 1 111.0 460.2 111.0 460.2 ; C21 C22 C23
> >
> > 41 42 43 1 111.0 460.2 111.0 460.2 ; C22 C23 C24
> >
> > 42 43 44 1 111.0 460.2 111.0 460.2 ; C23 C24 C25
> >
> > 43 44 45 1 111.0 460.2 111.0 460.2 ; C24 C25 C26
> >
> > 44 45 46 1 111.0 460.2 111.0 460.2 ; C25 C26 C27
> >
> > 45 46 47 1 111.0 460.2 111.0 460.2 ; C26 C27 C28
> >
> > 46 47 48 1 111.0 460.2 111.0 460.2 ; C27 C28 C29
> >
> > 47 48 49 1 111.0 460.2 111.0 460.2 ; C28 C29 C9
> >
> > 48 49 50 1 111.0 460.2 111.0 460.2 ; C29 C9 C10
> >
> > [ dihedrals ]
> >
> > ; ai aj ak al fu c0, c1, m, ...
> >
> > 16 15 18 17 2 0.0 1673.6 0.0 1673.6 ; imp C32 C33 O31 O46
> >
> > 34 33 36 35 2 0.0 1673.6 0.0 1673.6 ; imp C16 O15 C17 O30
> >
> > 19 18 32 20 2 35.3 836.8 35.3 836.8 ; imp C13 O31 C14 C12
> >
> > 22 21 24 23 2 35.3 836.8 35.3 836.8 ; imp P8 O11 O9 O10
> >
> > 28 27 29 30 2 35.3 836.8 35.3 836.8 ; imp N1 C2 C6 C5
> >
> > 4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C44 C45 C1 C8
> >
> > 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih C43 C44 C45 C1
> >
> > 6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih C42 C43 C44 C45
> >
> > 7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih C41 C42 C43 C44
> >
> > 8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C40 C41 C42 C43
> >
> > 9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C39 C40 C41 C42
> >
> > 10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih C38 C39 C40 C41
> >
> > 11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C37 C38 C39 C40
> >
> > 12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C36 C37 C38 C39
> >
> > 13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih C35 C36 C37 C38
> >
> > 14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih C34 C35 C36 C37
> >
> > 15 14 13 12 1 0.0 5.9 3 0.0 5.9 3 ; dih C33 C34 C35 C36
> >
> > 16 15 14 13 1 0.0 5.9 3 0.0 5.9 3 ; dih C32 C33 C34 C35
> >
> > 14 15 16 18 1 0.0 0.4 6 0.0 0.4 6 ; dih C34 C33 C32 O31
> >
> > 15 16 18 19 1 180.0 16.7 2 180.0 16.7 2 ; dih C33 C32 O31 C13
> >
> > 32 19 18 16 1 0.0 3.8 3 0.0 3.8 3 ; dih C14 C13 O31 C32
> >
> > 18 19 20 21 1 0.0 5.9 3 0.0 5.9 3 ; dih O31 C13 C12 O11
> >
> > 33 32 19 18 1 0.0 5.9 3 0.0 5.9 3 ; dih O15 C14 C13 O31
> >
> > 22 21 20 19 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O11 C12 C13
> >
> > 20 21 22 25 1 0.0 1.0 3 0.0 1.0 3 ; dih C12 O11 P8 O4
> >
> > 20 21 22 25 1 0.0 3.1 2 0.0 3.1 2 ; dih C12 O11 P8 O4
> >
> > 26 25 22 21 1 0.0 1.0 3 0.0 1.0 3 ; dih C3 O4 P8 O11
> >
> > 26 25 22 21 1 0.0 3.1 2 0.0 3.1 2 ; dih C3 O4 P8 O11
> >
> > 22 25 26 27 1 0.0 3.8 3 0.0 3.8 3 ; dih P8 O4 C3 C2
> >
> > 28 27 26 25 1 0.0 5.9 3 0.0 5.9 3 ; dih N1 C2 C3 O4
> >
> > 26 27 28 31 1 0.0 3.8 3 0.0 3.8 3 ; dih C3 C2 N1 C7
> >
> > 19 32 33 34 1 0.0 3.8 3 0.0 3.8 3 ; dih C13 C14 O15 C16
> >
> > 32 33 34 36 1 180.0 16.7 2 180.0 16.7 2 ; dih C14 O15 C16 C17
> >
> > 37 36 34 33 1 0.0 0.4 6 0.0 0.4 6 ; dih C18 C17 C16 O15
> >
> > 38 37 36 34 1 0.0 5.9 3 0.0 5.9 3 ; dih C19 C18 C17 C16
> >
> > 39 38 37 36 1 0.0 5.9 3 0.0 5.9 3 ; dih C20 C19 C18 C17
> >
> > 40 39 38 37 1 0.0 5.9 3 0.0 5.9 3 ; dih C21 C20 C19 C18
> >
> > 41 40 39 38 1 0.0 5.9 3 0.0 5.9 3 ; dih C22 C21 C20 C19
> >
> > 42 41 40 39 1 0.0 5.9 3 0.0 5.9 3 ; dih C23 C22 C21 C20
> >
> > 43 42 41 40 1 0.0 5.9 3 0.0 5.9 3 ; dih C24 C23 C22 C21
> >
> > 44 43 42 41 1 0.0 5.9 3 0.0 5.9 3 ; dih C25 C24 C23 C22
> >
> > 45 44 43 42 1 0.0 5.9 3 0.0 5.9 3 ; dih C26 C25 C24 C23
> >
> > 46 45 44 43 1 0.0 5.9 3 0.0 5.9 3 ; dih C27 C26 C25 C24
> >
> > 47 46 45 44 1 0.0 5.9 3 0.0 5.9 3 ; dih C28 C27 C26 C25
> >
> > 48 47 46 45 1 0.0 5.9 3 0.0 5.9 3 ; dih C29 C28 C27 C26
> >
> > 49 48 47 46 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C29 C28 C27
> >
> > 50 49 48 47 1 0.0 5.9 3 0.0 5.9 3 ; dih C10 C9 C29 C28
> >
> >
> >
> >
> >
> > title = vals
> >
> > cpp = /usr/bin/cpp
> >
> > define = -DFLEXIBLE
> >
> > constraints = none
> >
> > integrator = steep
> >
> > dt = 0.002 ; ps !
> >
> > nsteps = 500
> >
> > nstlists = 10
> >
> > ns_type = grid
> >
> > rlist = 1.0
> >
> > coulombtype = PME
> >
> > rcoulomb = 1.0
> >
> > vdwtype = cut-off
> >
> > rvdw = 1.0
> >
> > fourierspacing = 0.12
> >
> > fourier_nx = 0
> >
> > fourier_ny = 0
> >
> > fourier_nz = 0
> >
> > pme_order = 4
> >
> > ewald_rtol = 1e-5
> >
> > optimize_fft = yes
> >
> > ;
> >
> > ; Energy minimizing
> >
> > ;
> >
> > emtol = 100.0
> >
> > emsteps = 0.01
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> > Gesendet von Yahoo! Mail
> >
> <http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52427/*http://de.overview.mail.yahoo.com>.
>
> >
> > Dem pfiffigeren Posteingang.
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================*
>
>
> ------------------------------------------------------------------------
> Gesendet von Yahoo! Mail
> <http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52427/*http://de.overview.mail.yahoo.com>.
>
> Dem pfiffigeren Posteingang.
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list