Hi Chris, Yes, the bondtypes, etc. sections go in the .itp file. The only way (I know of) to respond to a specific thread is to have an email from that thread. Bob
On 7/26/07, Christopher Stiles <[EMAIL PROTECTED]> wrote: > Yang, > Thank you again for being so detailed. I do have 2 questions though, > when you say: > >So you shall change ffG43b1.itp to ffgmx.itp. And add the line > >C C 1 0.14210 478900. > > > >To the end of section [ bondtypes ], not the end of the whole file. > You mean in the topology file I assume for the changing from ffG43b1.itp to > ffgmx.itp. But the adding of the line is what I am having trouble with, > should it go in the topology file or ffgmx.itp? because neither have a > [ bondtypes ] section and when I add one it just gives me errors. From what > I understand from the manual it is only the *.itp files that can have those > sections, so I think maybe it should go in the ffgmx.itp file I am just not > making the addition to the file properly. > Also here is a copy of the ffgmx.itp file: > ######################## > #define _FF_GROMACS > #define _FF_GROMACS1 > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 no 1.0 1.0 > > #include "ffgmxnb.itp" > #include "ffgmxbon.itp" > ######################## > And here is a copy of my ffG43b1.itp file: > ######################## > #define _FF_GROMOS96 > #define _FF_GROMOS43B1 > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 no 1.0 1.0 > > #include "ffG43b1nb.itp" > #include "ffG43b1bon.itp" > ######################## > > Last of all this question is to any one, how do I reply to a specific > thread? I have searched around and I have had no luck. > > Thank you so much for all of your help! > > ~Christopher Stiles > College of Nanoscale Science and Engineering (CNSE) > State University of New York, Albany, New York 12203, USA > > _______________________________________________________ > > Hi, > > I missed one dash in the front. So it should be > > include = -IffG43b1.n2t > > The problem you had was because of improper usage of include, for every item > to be put in include=, you shall prefix -I in the front. Since you have not > put it, cpp couldn't finish parsing the topology file, so your topology > contains nothing. > > ffG43b1.n2t is not necessary for grompp. > > You shall include spc.itp in your topology file to include the topology for > water. So your file header shall be like > > #include "ffG43b1.itp" > #include "spc.itp" > > Last and most important, the line you added to ffgmxbon.itp is useless > because you are using GROMOS96 force field. > > So you shall change ffG43b1.itp to ffgmx.itp. And add the line > C C 1 0.14210 478900. > > To the end of section [ bondtypes ], not the end of the whole file. > > So the command line without -maxwarn can work properly. Note that you shall > not use -maxwarn in most cases. > grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p > SWNT_6_6_144_post_genbox.top -pp > > The suffix _s is just what I have specified for my build. You don't need the > same setting. > > Regards, > Yang Ye > > > On 7/25/2007 10:29 PM, Christopher Stiles wrote: > > Yang, > > Thank you very much for you help. I am sorry I did not think to package my > > files and commands up I will do so by the end of the day. As to the > > ffG43b1.n2t it was to get x2top to work, it defines single and double > bonded > > carbon so that I do not have to cap my tube with hydrogen. Although I am > not > > sure how you got the include to work with: > > include = IffG43b1.n2t > > Do you have a file named IffG43b1.n2t in your lib or your working dir? > > The file comes from the ffgmx.n2t file in the Gromacs lib but the name is > > changes to ffG43b1.n2t and the following 2 lines are added: > > C C 1 C ; CNT Carbon with one > bond > > C C 2 C C ; CNT double bonded > Carbon > > Next must I use grompp_s? (I believe this is grompp with single accuracy, > > correct?) Because if so I will have to compile it. > > Last question, by it gives a pass do you mean you get a little over 1500 > > warnings and then get the following: > > Fatal error: > > No such moleculetype SOL > > > > Thank you so much for your help I really appreciate it, > > > > ~Christopher Stiles > > College of Nanoscale Science and Engineering (CNSE) > > State University of New York, Albany, New York 12203, USA > > > > > > > >> Hi, > >> > >> Sorry that most of us on the list were too busy to read one full page of > >> details and download individual files. We might just prefer to download > >> one package, and run a script file for us quickly dive into the problem. > >> > >> Is include in mdout_test.mdp a standard option? Where did you get it? I > >> changed it to > >> > >> include = IffG43b1.n2t > >> > >> It works. Otherwise, cpp terminates before it generates a full top. > >> grompp -pp is always a good friend for grompp error (and thorough > >> reading of chapter 5 of manual). > >> > >> Next issue comes the format of ffG43b1.n2t. I don't think it conforms to > >> any GROMACS topology format. Again where does it comes from? > >> > >> My grompp command line: > >> grompp_s -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p > >> SWNT_6_6_144_post_genbox.top -maxwarn 10000000 -pp > >> > >> It gives a pass, at least. > >> > >> Hope you can work further on. > >> > >> Regards, > >> Yang Ye > >> > >> On 7/25/2007 2:41 AM, Christopher Stiles wrote: > >> > >>> I am trying to simulate a single wall carbon nanotube in a box > >>> solvated in water, at 300k for about 200ps. Also once I accomplish > >>> this I wish to fix either one end of the tube or fix the center of > >>> mass position, although this part is unimportant if I can not get the > >>> thing to run at all yet. > >>> > >>> I have created a page with a full detailed account of what I have done > >>> and tried so far. http://cs86.com/CNSE/SWNT.htm > >>> > >>> Please note all files where created with Vim in the unix environment > >>> so I think I have eliminated the formatting issues. > >>> > >>> Also that I have tried the simulation with many different sized tubes > >>> from TubeGen (http://turin.nss.udel.edu/research/tubegenonline.html ), > >>> both with and without hydrogen capped ends (this is something I have > >>> read in the archives as a possible solution, it makes no difference in > >>> the end). > >>> > >>> I have come to the conclusion through the help of many of you that the > >>> *.pdb file from TubeGen and mainly the residue UNK among other > >>> things. If any one has had luck with using a TubeGen file to create a > >>> simulation please let me know as to how. Other wise I am looking at a > >>> few new options basically all of them involve writing my own files. > >>> > >>> I guess I am looking for advice where to go from here. > >>> > >>> ~Christopher Stiles > >>> College of Nanoscale Science and Engineering (CNSE) > >>> State University of New York, Albany, New York 12203, USA > >>> > > > > > > _______________________________________________ > > 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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > ------------------------------ > > _______________________________________________ > 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! > > > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ 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! 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