Thanks very much for much for your help. The Carbon naotube issue is solved. I still have to figure out the polymers. Thanks for the info Regards Elie
> Date: Fri, 14 Sep 2012 10:31:28 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Segmentation fault (core dumped error) > > > > 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 > > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
