Re: [gmx-users] regarding generation of a topology file using Topolbuild
On Thu, 9 Oct 2014 at 3:00 PM, Sahithya S Iyer sah2...@gmail.com wrote: Hello users I am trying to generate a topology for CHL (chlorophyll a) using oplsaa ff. I am using topolbuild1_3 as an automated tool suggested in the Protein-Ligand Tutorial by Justin A. Lemkul to generate topology using oplsaa ff. I have converted the pdb file of Chl a to mol2 file ( both of the files attached herein). On running the mol2 file, it gives the following error - Fatal error. Source code file: readmol2.c, line: 765 Atom 3 (CHB) has 2 connections when required to have 3 Can you please guide me as to how this error can be rectified ? Thanks in advance. The attachment was not passed on. Topolbuild tries to check for consistent chemistry because the rules for selecting atom types will fail if the mol2 atom types are not consistent with the bonding structure given in the mol2 file. The error message means that atom number 3 does not have enough bonds to it for the atom type specified in the mol2 file. This means there is an error in how the mol2 file was generated. There may be more errors in the mol2 file beyond atom 3 because that error was so severe. I usually use either Chimera or Avogadro to save mol2 files, but with these, the type of the guanidino carbon of arginine needs to be changed to C.cat to meet the Sybyl mol2 specifications. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St., Rm. LD-061 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.
[gmx-users] I am still being regularly unsubscribed from the gromacs.org mailing list
On April 24, May 5, May 11, May 26, and at 1AM on June 10, I have received messages with the subject, You have been unsubscribed from the gromacs.org_gmx-users mailing list. These e-mail do not have any text to them at all. I immediately resubscribe myself only to receive another subsequently. I do not believe that I have done anything wrong on the mailing list. What is causing this? What do I need to do to stop this from taking place? -- 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.
[gmx-users] I keep receiving messages that I have been unsubscribed from the mailing list.
On April 24, May 5, and May 11, I have received messages with the subject, You have been unsubscribed from the gromacs.org_gmx-users mailing list. These e-mail do not have any text to them at all. I immediately resubscribe myself only to receive another the following week. I do not believe that I have done anything wrong on the mailing list. What is causing this? -- 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.
Re: [gmx-users] topolbuild
On Sunday, May 4, 2014, at 3:04 AM Hossein Lanjanian hossein.lanjan...@gmail.com wrote: hi We installed topolbuild topolbuild version 1.3 Command line: /home/Hossein/Desktop/topolbuild1_3/src/topolbuild -n test -dir ./topolbuild1_3/dat/gromacs -ff oplsaa Fatal error. Source code file: readmol2.c, line: 639 Incomplete mol2 file after bonds record.: we would like to know, what is the origin of this error. -- With The Best H.Lanjanian --- Hossein Lanjanian, Ph.D. student Laboratory of Systems Biology and Bioinformatics (LBB) Institute of Biochemistry and Biophysics (IBB), University of Tehran Tehran, Iran http://LBB.ut.ac.ir http://ibb.ut.ac.ir h.lanjan...@ut.ac.ir Your mol2 file does not have any mol2 lines after the bonds records. At the end of the bonds list, a proper mol2 file has a line that begins with, @TRIPOS and ends with the unix end of line. For most mol2 files, this is line reads, @TRIPOSSUBSTRUCTURE, but unless the mol2 file header record calls for some form of restraints, the program only checks for the initial tag. To correct your file, you only need to add the appropriate line, terminated by an end of line, to your file. I hope that 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.
Re: [gmx-users] how to add parameters to Topolbuild
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.
