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

[rasoul nasiri]

P.S,
You can E-mail your request to cgmartini at rug.nl.

Rasoul


On Fri, Jan 29, 2010 at 10:18 AM, rasoul nasiri <nasiri1355 at gmail.com>wrote:

> 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/20100129/2d806353/attachment.html>