On Wednesday, January 1, 2014 at 6:33 PM, Tom <dna...@gmail.com> wrote: > Can someone help us about how to add misssing parameters > into Topolbuild? > > We are using topolbuild to build *top file for a molecular which > has amide group. > > Topolbuld reports missing parameters of bonding, angle and dihedral. > ---------------------------- > missing bond parameters of (C-N); > 11 13 ; N7- C8 > 27 29 ; C6p- N9 > 45 47 ; N12p- C10 > > mising angle parameters of of CA-N-C, C-N-H, N-C-CA and N-C-O.: > 7 11 13 ; C4- N7- C8 > 13 11 12 ; C8- N7- H7 > 11 13 14 ; N7- C8- C1p > 11 13 23 ; N7- C8- O12 > > 20 27 29 ; C5p- C6p- N9 > 29 27 28 ; N9- C6p- O13 > 27 29 30 ; C6p- N9- H9 > 27 29 31 ; C6p- N9- C7p > > 38 45 47 ; C11p- N12p- C10 > 47 45 46 ; C10- N12p- H12p > 45 47 48 ; N12p- C10- C13p > 45 47 57 ; N12p- C10- O18 > ----------------------------------------- > Even we manually add these paramters into the ffoplsaa.dat in the > default directory. > Topolbuild can recognized the bonds and angles but still > can not write the > parameters onto *top file.
First, topolbuild does not read the gromacs default directory or the gromacs files. Your command line had to give the directory that contains topolbuild specific files ATOMTYPE_OPLSAA1.DEF, ATOMTYPE_oplsaa.DEF and ffoplsaa.dat Note that this ffoplsaa.dat is a special topolbuild specific text file and not anything like the gromacs ffoplsaa.dat However, this format is still text and can be edited with a text editor. To add parameters to this file, one must know how many parameter lines are to be added to each type of parameter. At the top of each section is a descriptive comment. For bonds, that reads ; Bond lengths and forces For angles, that reads ; angles phases and forces Below each comment is a text line that gives a count. For example bonds 258 or angles 789 Whenever entries are added or removed, this count must be updated to reflect the current number of entries of that type. I use this count for memory allocation for the assignment process. In what follows I will use the parameters you listed in your message for the example. At the bottom of the bonds entries add your bonds line as (all one line): C N 1 0.133500 410032.0 ; 259 Then change the bonds count to 259 At the bottom of the angles entries, add your angles lines as (4 lines): CA C N 1 115.500 585.760 ; 790 O C N 1 120.400 669.440 ; 791 CA N C 1 121.900 418.400 ; 792 C N H 1 119.800 292.880 ; 793 Then change the angles count to 793 These edits to the topolbuild parameters file in /your_topolbuild_directory/dat/gromacs/ffoplsaa.dat should enable topolbuild 1.3.1 to put all the entries into the topology. Please remember to edit the *.top file that results to reflect the change in location of gromacs forcefield files that came with gromacs 4.* because topolbuild 1.3.1 was written back when gromacs 3.3 was the current version. > Thanks a lot for your help! I hope this helps. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- 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.