[gmx-users] Difficulty preparing a polymer (PEG) for simulation

Mark Abraham mark.j.abraham at gmail.com
Thu Mar 27 21:25:16 CET 2014


On Mar 27, 2014 3:25 PM, "Dan Sponseller" <gromacs at danpeg.com> wrote:
>
> I'm trying to prepare PEG for simulation in gromacs and running into
> considerable difficulties. My PEG chain is
>
> HOC-COC-COC......COC-COC-COH
>
> with appropriate hydrogens on the carbons. I am using the new CHARM36.ff
> Following the procedure for polymers, I added a beginning, and end, and a
> central chain piece to 'merged.rtp' and modified the atom names in the
.pdb
> file to match. I have also added the residues to the 'residuetypes.dat' as
> Non-Protein (I have also tried listing it as a Protein).
>
> pdb2gmx claims I have169 missing atoms but will create the .gro and .top
> files anyway with the -missing parameter passed. The .gro file has all the
> atoms but the .top seems to be missing much information on bonds and
angles.
> Probably no point in continuing but after a quick editconfig, grompp gives
> me a fatal error: Group Protein referenced in the .mdp file was not found
in
> the index file.

Well that one is easy - refer in the .mdp to the thing that is there, not
what is not!

> I am new to gromacs and would really appreciate help getting started on
its
> use like this. Following is some of my data files.
>
> Daniel Sponseller
> PhD student
> Computational Science and Informatics
> George Mason University
>
>
>
>
********************************************************************************
> Snip from 'merged.rtp'
>
> ;Dan Sponseller
> ;Copying from DME below for the repeating chain for PEG.
> [ LIG ]
>  [ atoms ]
>           C1 CC32A   -0.010  0
>          H11 HCA2A    0.090  1
>          H12 HCA2A    0.090  2
>          OO2 OC30A   -0.340  3
>           C3 CC32A   -0.010  4
>          H31 HCA2A    0.090  5
>          H32 HCA2A    0.090  6
>  [ bonds ]
>           C1   -C3
>           C1   H11
>           C1   H12
>           C1   OO2
>          OO2    C3
>           C3   H31
>           C3   H32
>           C3   +C1
>
> ;Dan Sponseller
> ;Next, define begining of chain for PEG. CH2-OH from [ ETOH ]
> [ LIGb ]
>  [ atoms ]
>          OO1 OG311   -0.650  0
>          H11  HGP1    0.420  1
>           C3 CG321    0.050  2
>           H31  HGA2    0.090  3
>           H32  HGA2    0.090  4
>  [ bonds ]
>          OO1   H11
>          OO1    C3
>           C3   H31
>           C3   H32
>           C3   +C1
>
> ;Dan Sponseller
> ;Next, define ending of chain for PEG. CH2-OH from [ ETOH ]
> [ LIGe ]
>  [ atoms ]
>           C1 CG321    0.050  0
>          H11  HGA2    0.090  1
>          H12  HGA2    0.090  2
>          OO2 OG311   -0.650  3
>          H21  HGP1    0.420  4
>  [ bonds ]
>           C1   -C3
>           C1   H11
>           C1   H12
>           C1   OO2
>          OO2   H21

Those files above seem fine, but pdb2gmx will have a hard time unscrambling
your input .pdb file, which lists the atoms of "end" residue at the
beginning and end, the "beginning" residue at the end, and interleaves
residue numbering throughout. Those are probably not all deal breakers, but
their combination is! An orderly progression from beginning to end is
expected.

Mark
********************************************************************************
> my modified 'PEG.pdb' file:
>
> COMPND    UNNAMED
> AUTHOR    GENERATED BY OPEN BABEL
> HETATM    1   C1 LIGe    1     -14.784  -1.665   0.506  1.00  0.00
> C
> HETATM    2   C3 LIG     2     -13.927  -1.410  -0.735  1.00  0.00
> C
> HETATM    3  OO2 LIG     2     -13.056  -0.302  -0.493  1.00  0.00
> O
> HETATM    4  H11 LIGe    1     -15.383  -2.563   0.355  1.00  0.00
> H
> HETATM    5  H12 LIGe    1     -14.137  -1.802   1.372  1.00  0.00
> H
> HETATM    6  H31 LIG     2     -13.333  -2.297  -0.956  1.00  0.00
> H
> HETATM    7  H32 LIG     2     -14.573  -1.185  -1.584  1.00  0.00
> H
> HETATM    8   C1 LIG     2     -12.207   0.022  -1.596  1.00  0.00
> C
> HETATM    9   C3 LIG     3     -11.325   1.216  -1.227  1.00  0.00
> C
> HETATM   10  OO2 LIG     3     -10.441   0.845  -0.167  1.00  0.00
> O
> HETATM   11  H12 LIG     2     -11.578  -0.836  -1.835  1.00  0.00
> H
> HETATM   12  H11 LIG     2     -12.818   0.276  -2.463  1.00  0.00
> H
> HETATM   13  H31 LIG     3     -10.741   1.519  -2.096  1.00  0.00
> H
> HETATM   14  H32 LIG     3     -11.953   2.046  -0.903  1.00  0.00
> H
> HETATM   15   C1 LIG     3      -9.568   1.894   0.257  1.00  0.00
> C
> HETATM   16   C3 LIG     4      -8.673   1.387   1.389  1.00  0.00
> C
> HETATM   17  OO2 LIG     4      -7.815   0.358   0.894  1.00  0.00
> O
> HETATM   18  H11 LIG     3      -8.949   2.211  -0.582  1.00  0.00
> H
> HETATM   19  H12 LIG     3     -10.160   2.738   0.611  1.00  0.00
> H
> HETATM   20  H31 LIG     4      -8.070   2.210   1.772  1.00  0.00
> H
> HETATM   21  H32 LIG     4      -9.294   0.988   2.192  1.00  0.00
> H
> HETATM   22   C1 LIG     4      -6.933  -0.187   1.877  1.00  0.00
> C
> HETATM   23   C3 LIG     5      -6.066  -1.274   1.239  1.00  0.00
> C
> HETATM   24  OO2 LIG     5      -5.215  -0.687   0.252  1.00  0.00
> O
> HETATM   25  H11 LIG     4      -6.294   0.603   2.270  1.00  0.00
> H
> HETATM   26  H12 LIG     4      -7.517  -0.619   2.690  1.00  0.00
> H
> HETATM   27  H32 LIG     5      -5.457  -1.751   2.007  1.00  0.00
> H
> HETATM   28  H31 LIG     5      -6.707  -2.020   0.768  1.00  0.00
> H
> HETATM   29   C1 LIG     5      -4.360  -1.621  -0.408  1.00  0.00
> C
> HETATM   30   C3 LIG     6      -3.499  -0.885  -1.437  1.00  0.00
> C
> HETATM   31  OO2 LIG     6      -2.622   0.020  -0.764  1.00  0.00
> O
> HETATM   32  H12 LIG     5      -3.715  -2.105   0.325  1.00  0.00
> H
> HETATM   33  H11 LIG     5      -4.965  -2.374  -0.913  1.00  0.00
> H
> HETATM   34  H32 LIG     6      -2.910  -1.608  -2.002  1.00  0.00
> H
> HETATM   35  H31 LIG     6      -4.143  -0.329  -2.118  1.00  0.00
> H
> HETATM   36   C1 LIG     6      -1.769   0.762  -1.639  1.00  0.00
> C
> HETATM   37   C3 LIG     7      -0.879   1.694  -0.814  1.00  0.00
> C
> HETATM   38  OO2 LIG     7       0.000   0.916   0.000  1.00  0.00
> O
> HETATM   39  H12 LIG     6      -1.145   0.073  -2.208  1.00  0.00
> H
> HETATM   40  H11 LIG     6      -2.377   1.353  -2.324  1.00  0.00
> H
> HETATM   41  H31 LIG     7      -0.293   2.323  -1.484  1.00  0.00
> H
> HETATM   42  H32 LIG     7      -1.502   2.323  -0.178  1.00  0.00
> H
> HETATM   43   C1 LIG     7       0.879   1.694   0.814  1.00  0.00
> C
> HETATM   44   C3 LIG     8       1.769   0.762   1.639  1.00  0.00
> C
> HETATM   45  OO2 LIG     8       2.622   0.020   0.764  1.00  0.00
> O
> HETATM   46  H11 LIG     7       1.502   2.323   0.178  1.00  0.00
> H
> HETATM   47  H12 LIG     7       0.293   2.323   1.484  1.00  0.00
> H
> HETATM   48  H32 LIG     8       2.377   1.353   2.324  1.00  0.00
> H
> HETATM   49  H31 LIG     8       1.145   0.073   2.208  1.00  0.00
> H
> HETATM   50   C1 LIG     8       3.499  -0.885   1.437  1.00  0.00
> C
> HETATM   51   C3 LIG     9       4.360  -1.621   0.408  1.00  0.00
> C
> HETATM   52  OO2 LIG     9       5.215  -0.687  -0.252  1.00  0.00
> O
> HETATM   53  H12 LIG     8       4.143  -0.329   2.118  1.00  0.00
> H
> HETATM   54  H11 LIG     8       2.910  -1.608   2.002  1.00  0.00
> H
> HETATM   55  H32 LIG     9       4.965  -2.374   0.913  1.00  0.00
> H
> HETATM   56  H31 LIG     9       3.715  -2.105  -0.325  1.00  0.00
> H
> HETATM   57   C1 LIG     9       6.066  -1.274  -1.239  1.00  0.00
> C
> HETATM   58   C3 LIG    10       6.933  -0.187  -1.877  1.00  0.00
> C
> HETATM   59  OO2 LIG    10       7.815   0.358  -0.894  1.00  0.00
> O
> HETATM   60  H12 LIG     9       6.707  -2.020  -0.768  1.00  0.00
> H
> HETATM   61  H11 LIG     9       5.457  -1.751  -2.007  1.00  0.00
> H
> HETATM   62  H31 LIG    10       7.517  -0.619  -2.690  1.00  0.00
> H
> HETATM   63  H32 LIG    10       6.294   0.603  -2.270  1.00  0.00
> H
> HETATM   64   C1 LIG    10       8.673   1.387  -1.389  1.00  0.00
> C
> HETATM   65   C3 LIG    11       9.568   1.894  -0.257  1.00  0.00
> C
> HETATM   66  OO2 LIG    11      10.441   0.845   0.167  1.00  0.00
> O
> HETATM   67  H11 LIG    10       9.294   0.988  -2.192  1.00  0.00
> H
> HETATM   68  H12 LIG    10       8.070   2.210  -1.772  1.00  0.00
> H
> HETATM   69  H31 LIG    11      10.160   2.738  -0.611  1.00  0.00
> H
> HETATM   70  H32 LIG    11       8.949   2.211   0.582  1.00  0.00
> H
> HETATM   71   C1 LIG    11      11.325   1.216   1.227  1.00  0.00
> C
> HETATM   72   C3 LIG    12      12.207   0.022   1.596  1.00  0.00
> C
> HETATM   73  OO2 LIG    12      13.056  -0.302   0.493  1.00  0.00
> O
> HETATM   74  H11 LIG    11      11.953   2.046   0.903  1.00  0.00
> H
> HETATM   75  H12 LIG    11      10.741   1.519   2.096  1.00  0.00
> H
> HETATM   76  H32 LIG    12      12.818   0.276   2.463  1.00  0.00
> H
> HETATM   77  H31 LIG    12      11.578  -0.836   1.835  1.00  0.00
> H
> HETATM   78   C1 LIG    12      13.927  -1.410   0.735  1.00  0.00
> C
> HETATM   79   C3 LIGb   13      14.784  -1.665  -0.506  1.00  0.00
> C
> HETATM   80  OO1 LIGb   13      15.647  -0.548  -0.727  1.00  0.00
> O
> HETATM   81  H12 LIG    12      14.573  -1.185   1.584  1.00  0.00
> H
> HETATM   82  H11 LIG    12      13.333  -2.297   0.956  1.00  0.00
> H
> HETATM   83  H32 LIGb   13      15.383  -2.563  -0.355  1.00  0.00
> H
> HETATM   84  H31 LIGb   13      14.137  -1.802  -1.372  1.00  0.00
> H
> HETATM   85  H11 LIGb   13      16.221  -0.641  -1.500  1.00  0.00
> H
> HETATM   86  OO2 LIGe    1     -15.647  -0.548   0.727  1.00  0.00
> O
> HETATM   87  H21 LIGe    1     -16.221  -0.641   1.500  1.00  0.00
> H
> TER
> END
>
>
>
********************************************************************************
> snips from pdb2gmx:
>
> WARNING: atom C1 is missing in residue LIGe 1 in the pdb file
>
>
> WARNING: atom H11 is missing in residue LIGe 1 in the pdb file
>         You might need to add atom H11 to the hydrogen database of
building
> block LIGe
>         in the file merged.hdb (see the manual)
>
>
> WARNING: atom H12 is missing in residue LIGe 1 in the pdb file
>         You might need to add atom H12 to the hydrogen database of
building
> block LIGe
>         in the file merged.hdb (see the manual)
>
> There were 169 missing atoms in molecule Non-Protein
> Number of bonds was 35, now 24
> Generating angles, dihedrals and pairs...
> Making cmap torsions...There are    0 dihedrals,    0 impropers,   11
angles
>             0 pairs,       24 bonds and     0 virtual sites
> Total mass 546.656 a.m.u.
> Total charge 0.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.3#
>
> Writing coordinate file...
>
> Back Off! I just backed up PEG.gro to ./#PEG.gro.3#
>                 --------- PLEASE NOTE ------------
> You have successfully generated a topology from: PEG_dan2.pdb.
> The Charmm36 force field and the tip3p water model are used.
>                 --------- ETON ESAELP ------------
>
>
> --
> View this message in context:
http://gromacs.5086.x6.nabble.com/Difficulty-preparing-a-polymer-PEG-for-simulation-tp5015424.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list