Re: [gmx-users] Confusion about itp file generated by topolbuild
Thanks for your reply Justin, but my confusion in the first part is not being removed. If #define is outdated then is it that gromacs does not even consider those lines? Then how does gromacs use those force fields during grompp? Also, if somehow gormacs considers those force fields then where is the location of them. There is no force field with such names in the working directory, neither in topolbuild directory nor in gromacs top directory . Regards On Tuesday, June 3, 2014 6:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/3/14, 6:51 AM, Bikramjit Sharma wrote: Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER #define _FF_USER [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 #include ffbennb.itp #include ffusernb.itp What is the meaning of first 3 lines? Because there is no force field with any of these names (appeared in those lines) in the working directory and we are not assigning any path. So I am confused. Those #define statements are somewhat outdated; I don't think Gromacs uses them in any way. They used to be needed in old versions, but not any more. Also, following suggestions from gromacs user list (https://www.mail-archive.com/gmx-users@gromacs.org/msg12722.html), I have commented the last two lines of this itp file. So, the non bonded parameter file generated by topolbuild is not used. Is it correct? That depends on whether or not those files introduce any new parameters that your molecule needs. If they do, commenting them out isn't correct. If they only contain duplicate information already present in the parent force field, commenting them out is fine. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: Confusion about itp file generated by topolbuild
On Tuesday, June 3, 2014 4:55 PM, Bikramjit Sharma bikramjit_...@yahoo.com wrote: On Tuesday, June 3, 2014 4:32 PM, Bikramjit Sharma bikramjit_...@yahoo.com wrote: Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER #define _FF_USER [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 #include ffbennb.itp #include ffusernb.itp What is the meaning of first 3 lines? Because there is no force field with any of these names (appeared in those lines) in the working directory and we are not assigning any path. So I am confused. Also, following suggestions from gromacs user list (https://www.mail-archive.com/gmx-users@gromacs.org/msg12722.html), I have commented the last two lines of this itp file. So, the non bonded parameter file generated by topolbuild is not used. Is it correct? Thanks, Regards, Bikram On Tuesday, June 3, 2014 3:57 PM, Bikramjit Sharma bikramjit_...@yahoo.com wrote: Hi all, I tried to generate topology file for benzene (as a trial) using topolbuild1_3. The itp file generated is (ffben.itp in my case) #define _FF_GAFF #define _FF_AMBER #define _FF_USER [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 #include ffbennb.itp #include ffusernb.itp What is the meaning of first 3 lines? Because there is no force field with any of these names (appeared in those lines) in the working directory and we are not assigning any path. So I am confused. Also, following suggestions from gromacs user list (https://www.mail-archive.com/gmx-users@gromacs.org/msg12722.html), I have commented the last two lines of this itp file. So, the non bonded parameter file generated by topolbuild is not used. Is it correct? Thanks, Regards, Bikram -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
