[gmx-users] Martini Coarse Graining Segmentation Fault using g_fg2cg

[rasoul nasiri]

Hi,

It is better you plan this question in MARtini forum, there are experts that
can answer this question!
Please register in:
http://md.chem.rug.nl/cgmartini/index.php/user-platform/login

Rasoul

On Thu, Jan 28, 2010 at 1:43 PM, Emanuel Peter <
Emanuel.Peter at chemie.uni-regensburg.de> wrote:

> Dear Gromacs Users,
>
> I have performed the Martini Coarse Graining procedure for the
> simulation of two protein domains by using the two scripts atom2cg.awk
> and seq2itp.pl. Then I was able to perform my simulation of my coarse
> grained system. My problem is now to convert my final cg structure into
> an all atom structure. For this purpose I tried to use the tool g_fg2cg
> with the inputs containing my fine grained topology ,the coarse grained
> topology and my coarse grained structure file. But obviously all
> attempts to apply that tool ended up in a segmentation fault message. I
> also tried to convert my all atom structure into a cg structure which
> ended up with the same segmentation fault message. Could you give me
> some advice on that problem? Here is my screen output:
>  Option     Filename  Type         Description
> ------------------------------------------------------------
> -pfg LOV1_LOV2.pdb.top  Input        Topology file
> -pcg martini_v2.0_example.top  Input, Opt!  Topology file
>  -c lov1lov2_42ns_27.1.pdb  Input        Generic trajectory: xtc trr
> trj gro
>                                   g96 pdb
>  -o        out.gro  Output       Generic structure: gro g96 pdb xml
>
>      Option   Type  Value  Description
> ------------------------------------------------------
>      -[no]h   bool     no  Print help info and quit
>       -nice    int      0  Set the nicelevel
>          -n    int      0  1: fg2cg transformation, 0: cg2fg
> transformation
>        -wat    int      0  1: rewrites FG_CG water to true fg water;
>        -rad   real    0.3  A radius for random atom insertion;
>
> calling cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 3 bonded neighbours for Protein_B 1
> NOTE:
>  System has non-zero total charge: -2.999998e+00
>
> #   G96BONDS:   2738
> #  G96ANGLES:   3994
> #      PDIHS:   1465
> #      IDIHS:   1328
> #       LJ14:   4520
> calling cpp...
> processing topology...
> Generated 0 of the 465 non-bonded parameter combinations
> Excluding 1 bonded neighbours for Protein 1
> Excluding 1 bonded neighbours for ProteinB 1
> NOTE:
>  System has non-zero total charge: -6.000000e+00
>
>
> Number of fg atoms 2696
> Number of cg atoms 571
> Reading frame       0 time 42000.004   1264673691
> Segmentation fault
>
> When I applied this tool on the ubiquitin example I had another problem,
> but I did it in the same way as before. Here is the screen output:
>
> Option     Filename  Type         Description
> ------------------------------------------------------------
> -pfg       1ubq.top  Input        Topology file
> -pcg       out3.top  Input, Opt!  Topology file
>  -c       1UBQ.gro  Input        Generic trajectory: xtc trr trj gro
> g96 pdb
>  -o        out.gro  Output       Generic structure: gro g96 pdb xml
>
>      Option   Type  Value  Description
> ------------------------------------------------------
>      -[no]h   bool     no  Print help info and quit
>       -nice    int      0  Set the nicelevel
>          -n    int      1  1: fg2cg transformation, 0: cg2fg
> transformation
>        -wat    int      0  1: rewrites FG_CG water to true fg water;
>        -rad   real    0.3  A radius for random atom insertion;
>
> calling cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 2 bonded neighbours for SOL 58
> #   G96BONDS:   766
> #  G96ANGLES:   1107
> #      PDIHS:   428
> #      IDIHS:   334
> #       LJ14:   1304
> #     SETTLE:   58
> calling cpp...
> cpp: out3.top: Datei oder Verzeichnis nicht gefunden
> cpp: warning: '-x c' after last input file has no effect
> cpp: no input files
> cpp exit code: 256
> Tried to execute: 'cpp
> -I/pc50417/pee18323/REVERSE_trans_gromacs/agromacs-reverse/share/top
> out3.top > grompp605Sk3'
> The 'cpp' command is defined in the .mdp file
> processing topology...
>
> Number of fg atoms 934
> Number of cg atoms 0
> Reading frames from gro file 'UBIQUITIN', 934 atoms.
> Reading frame       0 time    0.000   out.xtc
> Last frame          0 time    0.000
>
> Back Off! I just backed up out.gro to ./#out.gro.2#
>
> Cg structure computed !
>
> In that case out.gro did not contain any atoms.
>
> Thanks for any suggestions!
>
> Best regards,
>
> Emanuel Peter
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100129/fc29d86b/attachment.html>