Dear All, I am resubmitting my question below as I did not receive a response and am thinking that my previous e-mail was not recognized by the system or missed. Could someone please provide me with an answer to my questions below?
Many thanks. Darrell Koskinen On 4/2/2009, "<darre...@localhost>" <> wrote: >>Date: Wed, 01 Apr 2009 22:38:28 +0200 >>From: David van der Spoel <sp...@xray.bmc.uu.se> >>Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum) >> not recognizing bonds >>To: Discussion list for GROMACS users <gmx-users@gromacs.org> >>Message-ID: <49d3d0c4.4040...@xray.bmc.uu.se> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >>darre...@ece.ubc.ca wrote: >>> Dear All, >>> I have been trying to determine why I am experiencing problems when I run >>> a gromacs file through x2top. I have checked my gromacs file with VMD to >>> ensure that the file is correct and VMD validates that my file is >>> correct as I see the intended structure. Thus, the atoms are indeed >>> located within reasonable distance from each other such that x2top >>> should be recognizing the bonds. >>> >>> Here is an extract from my gromacs file: >>> >>> 2Grph C 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 >>> 2Grph C 2 0.071 -0.123 0.000 0.0000 0.0000 0.0000 >>> 2Grph C 3 0.071 0.123 0.000 0.0000 0.0000 0.0000 >>> 2Grph C 4 -0.142 0.000 0.000 0.0000 0.0000 0.0000 >>> 2Grph C 5 -0.000 -0.250 0.000 0.0000 0.0000 0.0000 >>> 2Grph C 6 0.210 -0.120 0.000 0.0000 0.0000 0.0000 >>> >>> I thought that in order to make x2top work correctly that I would have to >>> modify the files as described in Christopher Stiles website >>> (http://cs86.com/CNSE/SWNT.htm). I made the specified changes to the >>> following files and saved them in my working directory: >>> ffencadv.n2t >>> ffgmx.n2t >>> ffgmxbon.itp >>> >>> I also changed the name of ffgmxbon.itp to ffencadvbon.itp as I read in >>> one post that this file should be renamed as such. >>> >>> After all these changes, I still experience a problem when I run the >>> command: >>> x2top -ff select -f graphene_nm.gro -o graphene_nm.top >>> selecting option 7: Encad all-atom force field, using scaled-down vacuum >>> charges >>> >>> When I run the above command, I receive output telling me that the atoms >>> have 0 bonds. An extract of the output appears below for your reference. >>> Can not find forcefield for atom H-266 with 0 bonds >>> Can not find forcefield for atom H-267 with 0 bonds >>> Can not find forcefield for atom H-268 with 0 bonds >>> Can not find forcefield for atom H-269 with 0 bonds >>> Can not find forcefield for atom H-270 with 0 bonds >> >> >>Could there still be an error in your gro file, as it seems to contain >>only C, and the error message points to H. x2top might work slightly >>better in 4.0.x. And by the way, this tutorial may be slightly >>confusing. The only thing you need to do is edit the .n2t file >>corresponding to your force field. I don't recall what is supplied in >>3.3, but in 4.0 it is ffoplsaa.n2t. > >My gro file does contain H atoms as well. In my extract of the gro file I >only showed the first few lines of the gro file and these lines only >have C atoms. Note that I receive the same message for the C atoms (i.e. >"Can not find forcefield for atom C-1 with 0 bonds"). > >I actually created the files ffencadv.n2t & ffgmx.n2t in my working >directory since the only n2t file I could find in the gromacs directory >was the ffoplsaa.n2t file and the tutorial did not mention the >ffoplsaa.n2t file. Should I be modifying the ffoplsaa.n2t file instead? >If so, can you please provide me some direction on what needs to be >added to this file so that it recognizes the atoms in my graphene >structure as I looked at this file but do not understand what some of >the columns represent. > >Also, I thought that ffoplsaa was to be used for liquids and since my >simulation is in an air environment, I thought that I should be using >the encad force field in a vacuum and should therefore be modifying an >encad n2t file. Please correct me if I am wrong. > >Also, could you also please explain the purpose of the n2t file as I >looked in the gromacs manual and see no description of files with the >n2t extension and their purpose. > >Thanks again in advance. > >Darrell > >> >>> >>> ------------------------------------------------------- >>> Program x2top, VERSION 3.3.3 >>> Source code file: x2top.c, line: 206 >>> >>> Fatal error: >>> Could only find a forcefield type for 0 out of 270 atoms >>> ------------------------------------------------------- >>> >>> Could you please help me resolve this issue? >>> >>> Thank you in advance for your assistance. >>> >>> Darrell Koskinen >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.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-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >>-- >>David. >>________________________________________________________________________ >>David van der Spoel, PhD, Professor of Biology >>Dept. of Cell and Molecular Biology, Uppsala University. >>Husargatan 3, Box 596, 75124 Uppsala, Sweden >>phone: 46 18 471 4205 fax: 46 18 511 755 >>sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
