[gmx-users] Segmentation fault (core dumped error)

[Justin Lemkul]

On 9/14/12 12:19 AM, Elie M wrote:
>
> Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that.
> (1) In an attempt to form the topology files of CNTs and graphene (using x2top), i have found on the internet scripts  (by Andrea Minoia I guess). These constitute of adding .nt2, .rtp. and .itp files to the /Gromacs/share/Gromacs/top directory  (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and tried to execute x2top and I got the error:
> "......Entries in elements.dat: 218Looking whether force field files existOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name to type translationsGenerating bonds from distances...Segmentation fault (core dumped)"
> Can anyone please tell me the source of this error and how to fix it?

x2top is telling you it found nothing in the .n2t file.  Either the contents are 
nonexistent, formatted incorrectly, or you have a line ending issue (common with 
Windows OS - use dos2unix if necessary).

> (2) I will definitely need a top file for the polymers I will also be solvating. But I also have problems because the pdb file contains a LIG residue unrecognizable by Gromacs. I have asked this question before and I was advised to change some files accordingly but to be honest I am not really professional in that; I have asked someone who had a problem in the past but he did not know all the details because he ended up not using the modified force fields after all. Can anyone give me in details how to incorporate the residue "LIG" within the force field or let me know whom I can consult...A part of the pdb file with the residue LIG is:
> "COMPND    UNNAMEDAUTHOR    GENERATED BY OPEN BABEL 2.3.1HETATM    1  C   LIG     1       1.481  -1.276  -0.621  1.00  0.00           CHETATM    2  C   LIG     1       2.216  -2.370  -1.040  1.00  0.00           CHETATM    3  S   LIG     1       3.770  -2.409  -0.306  1.00  0.00           SHETATM    4  C   LIG     1       3.456  -0.998   0.609  1.00  0.00           CHETATM    5  C   LIG     1       2.207  -0.479   0.313  1.00  0.00           CHETATM    6  C   LIG     1       5.156   0.676   1.386  1.00  0.00           CHETATM    7  C   LIG     1       4.423  -0.491   1.600  1.00  0.00           CHETATM    8  C   LIG     1       4.550  -1.119   2.847  1.00  0.00           CHETATM    9  C   LIG     1       5.256  -0.503   3.905  1.00  0.00           CHETATM   10  C   LIG     1       6.107   0.592   3.667  1.00  0.00           CHETATM   11  C   LIG     1       6.008   1.181   2.393  1.00  0.00           CHETATM   12  S   LIG     1       7.457   2.548   5.198  1.00  0.00      !
      SHETA
TM   13  C   LIG     1       7.220   0.945   4.621  1.00  0.00        ..."

You need to introduce some sensible set of parameters for it.  Using a generic 
"LIG" for a polymer is unlikely to work.  Consult the following:

http://www.gromacs.org/Documentation/How-tos/Polymers
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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