Re: [gmx-users] AMBER to GROMACS conversion
On Tuesday, June 25, 2013 8:10 PM, Parker de Waal wrote: > Now I've been able to successfully convert the two .mol2 files into gromacs > .itp however I am unsure how to convert the .frcmod file as well. I'm sorry, but while topolbuild does convert *.mol2 files into gromacs *.itp files with AMBER parameters, it does not make use of AMBER files. Therefore, topolbuild 1.3 will not convert the *.frcmod files. You should edit your *.itp file with any text editor to change entries according to what is found in the desired *.frcmod file. I should also note that the output from topolbuild 1.3 requires some text editing to be made compatible with GROMACS versions greater than 4.0.* because the arrangement of parameter files within the GROMACS */share/gromacs/top directory was changed and topolbuild has not been updated for that change. Finally, I need to note that for AMBER forcefields in GROMACS naming of atom types was updated to be the standard AMBER atom type names with release of the GROMACS 4.5.* series, but topolbuild 1.3 does not reflect that change either. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Topolbuild configuration
On Sunday, December 9, 2012 at 7:48 PM SeokYun123 wrote: >I'm trying to download topolbuild1_2_1 in my Mac computer. First, why are you using 1.2.1 instead of 1.3 which is also available in the user contributed software section at gromacs.org? Actually, there should be a topolbuild1_3_1 contribution there as well. I don't know what happened to that release. Actually, topolbuild is not up to date with gromacs releases. >I understand that the executable file is in the same directory as the >Makefile. I also understand the thing about the PATH. Did you read INSTALLATION.txt in the main directory? >For different files I have downloaded, I was able to ./configure it and use >make, but for topolbuild, I wasn't able to ./configure it as it prints out >an error message. This is because there isn't a configure script at all for topolbuild Instead some sample makefiles are provided named Makefile and Makefile.G4OsX For your purposes, the supplied Makefile should work so you just need to type make to get an executable. Type make clean to clean up afterwards. >From the previous thread, I read that "Common practice is to then put it in >some central directory for executables (like /usr/local/bin, or some >subdirectory of your /home directory, depending on >your permissions on the system)." You can either leave the executable in the src directory where it is built, or you can move it to a desired directory. Please remember that the dat directory contains the parameters files that topolbuild needs in order to generate a topology. >I think that would help me fix my problem, but I'm not so sure how to do >this. > >Could anyone give me an advice regarding this issue? There are *.txt files in the main directory of each version of topolbuild to document how to install and how to use the program. Please remember that the topologies generated need further editing with a text editor for use with gromacs 4.5 and 4.6 releases because the organization of topology files changed with the 4.5 release and topolbuild has not been updated in a while. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] topolbuild and charges
On Friday, February 3, 2012 at 12:31 AM, Tom wrote: > Any one has the experience of topolbuild? > > I tried to build *top file with the software of topolbuild > > ./topolbuild -n lipid -dir >/home/computer/Tom/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff oplsaa > > I chose oplssaa. But from the generated *top file,these charges in *top file > can > not match the partial charges in file (in gromacs package) of > /opt/gromacs-4.5.4/share/gromacs/top/oplsaa.ff/ffnonbonded.itp > > How to understand these charges on *top file, which topolbuild generates? > Thanks for your instruction! First, topolbuild never "generates" charges. Unless the -charge option is specified, the charges come from whatever is read as being the charge entry in the *.mol2 file. If the charge type in the header of the *.mol2 file reads "INVALID", or "NO_CHARGE", the charges are reset to 0 as the *.mol2 file is read. If the -charge option is given, topolbuild assigns charges given in the "Atoms data" section of the force field parameters file in the directory pointed to by the -dir entry according to assigned atom type. In the case of oplsaa, the parameters file is ffoplsaa.dat, the column is labeled charge, and the assignment is based on oplsaa atom type number. All of this, of course, relies on the *.mol2 file being syntactically correct according to the rules given by Tripos, Inc. Some programs that attempt to write *.mol2 files fail to write complete Sybyl atom types. Others do write complete atom types, but sometimes have problems getting the atom type correct, most notably with the guanidino carbon of arginine which is supposed to be C.cat I hope this short note helps. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Thanks for your help!
I am replying to the Gromacs User's list rather than directly. On Monday, January 30, 2012 12:38 AM,Tom wrote: > Thanks for answering me my question and thanks for the nice open > source code program! > I found out my prvious problem due to the problem of my *mol2 file. > > Can you help with two more doubts? > > 1) Can you provide a reference for me if I want to cite your work of > topolbuild program? I have not published anything regarding topolbuild. As noted in the source code comments, when I wrote it, I borrowed heavily from other sources. > 2) i am making a chemical structure, which contains 2 hydrocarbon (surgar > ring) > connected with 2 H2PO4-. I tired to use topolbuild and oplsaa forcefield. I > noticed > oplss only has forcefield and partial charges MeOPO3H and MeOPO3--, but there > are no parameters available for H2PO4-. But the program of topolbuild works > magically > to assign the charges, by whichthe overal is -2, which is exactly equal to > the real > situation (the total charges of my *mol2 file is -2) although the type of P > is P??? Something has bothered me about the *.mol2 file excerpt you pasted in your original e-mail. It did not have correct Tripos atom types in the sixth column and totally lacked the seventh, eighth, and ninth columns that contain the atom segment number, the residue name, and the atom charge which should be 0.0 for a molecule with NO_CHARGE specified in the file heading. I can only assume that what you pasted in your original e-mail was not the file you actually used. > I want to consult you what kind of algorithm that you used to assign the > partial charges > and make the total equal to the expected value? The command you listed in your original e-mail would not assign charges, but would take the charges given in the *.mol2 file. For the excerpt of an *.mol2 that you pasted in your original e-mail, these charges would be 0.0 because the heading read NO_CHARGE If the -charge option is given in the command line, the charge for each atom type is read from the parameters file for the selected force field found in the directory pointed to by the -dir parameter. The charges in the paramters files for these atom types and force fields were copied from gromacs force field files. This is not in any way a sophisticated charge assignment. > If you have time and want to look at my *mol file and the generated *top > file, i can email > to you. I had been under the impression that you had pasted an excerpt from your actual *.mol2 file although I do not see how that file could have been accepted as a valid *.mol2 file by topolbuild -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: topolbuild1_3:Illegal characters for size information line in mol2 file.
On Thursday, January 26, 2012 at 12:50 AM, Tom wrote: > Dear Bruce and Gromacs Users, > > i am a new user of topolbuild. > I am trying to use topolbuild to build *top file, but there is a fatal error > report: > --- > ./topolbuild -n lipid -dir > /home/machine/TOM/Study/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff > oplsaa > Fatal error. > Source code file: readmol2.c, line: 347 > Illegal characters for size information line in mol2 file. > The error is on the line that reads 295 296 The error means that the line giving the number of atoms and number of bonds contains characters that are not any of the digits 0123456789, spaces, tabs, or the line feed that marks end of line. This typically happens when one has produced a Microsoft Windows compatible file that terminates lines with a carriage return and line feed or a Macintosh compatible file that terminates lines with carriage return instead of line feed. Probably the file was generated as Microsoft Windows compatible and you should run the dos2unix script on the file before submitting it to topolbuild. If this does not correct the problem, you will need to view the file in a unix text editor to see where the illegal characters are. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Regarding generating topology file.
On Tuesday, August 2, 2011 at 5:17 AM, Ravi Kumar Venkatraman wrote: > I have got some topology and parameter file for some small organic molecules from swissparam in *.mol2 format. > I am trying to generate *.top, *.gro & *.itp files using topolbuild. But I dont know how to do. So can anybody > give me a link or some materials related to this. I'm not sure what the problem is. The topolbuild 1.3.1 download does include documentation on how to use it. Is there something specific you have tried that you are having difficulties with? Of course, for use with gromacs 4.5.*, one does have edit the *.top with a text editor to change the initial include lines in the topology file to reflect the re-organization of the force field files. Furthermore, the current topolbuild version does not support CHARMm force fields. Also, I believe that swissparam gives those files. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] use AMBER ff03 force field in gromacs 4
On Thursday, May 12, 2011 at 9:03 AM"mirc...@sjtu.edu.cn" wrote: > I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I > encountered some > problems when generating the topology file of the ligands. I generate the > topology file > of ligands by using topolbuild package. The atom types of GAFF force field > are assigned > to the atoms of the ligand. However, when I used grompp command to write the > tpr file. > There is an error saying: > > Fatal error: > Atomtype c3 not found > For more information and tips for troubleshooting, please check the GROMACS > > > It seemed that, the amber ff03 force field in gromacs 4 didn't include the > atom types of > the GAFF force field. > > Does any one have ever encountered the same problem? What can I do to solve > this problem? > > It seemed that the atoms types in GAFF force field (e.g., c3, hx, hc, etc. ) can not > be recongnized by the amber ff03 FF implemented in gromacs 4.5.3. This is absolutely correct. GAFF atom types are not included in other amber force fields. However, for GAFF, the output of topolbuild includes an *nb.itp file that gives the atom types and the LJ parameters for those atom types. I've not tried mixing amber force fields like this, but I believe that if you include this up at the top after including your desired amber force field includes, everytihing should be defined correctly. I seem to recall others doing this already. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Problem with using topolbuild1_3.tgz
On Sat, Jan. 22, 2011 at 1:44 AM, Sweta Iyer wrote: > > On Thu, January 20, 2011 at 6:41PM, Sweta Iyer wrote: > >> Hi, I am trying to generate topology files for a set of lipids with the > >> help of topolbuild1_3.tgz package found at the other software page of > >> GROMACS website. > >> > >> I downloaded and installed all files and tried running the program with > >> a > >> MOL2 file with charges in it. However, it shows an error message as > >> follows: > >> > >> Fatal error. > >> Source code file: readmol2.c, line: 758 > >> Atom 1 (C) has 3 connections when allowed 0 > >> > >> I am not sure how to get over this problem! Wonder what will fix this > >> error and get the program running! > > > > A major requirement of topolbuild is that the mol2 file use correct atom > > types as defined by Tripos, whose file format mol2 is, and as used in > > Sybyl. > > The error message suggests that you have not specified correct Tripos > > Sybyl > > atom types. There may be other problems in your mol2 file as well. > > Correct the atom types and check that the file is otherwise syntactically > > correct and it should work. > > > > However, I believe that lipid topology files for gromacs are already >available > > for download. > > > > I hope that helps. > > Hi Bruce, > Thanx for the reply. The MOL2 file was generated by the RESP ESP charge > derive server. I did not check the file in SYBYL. However, structurally it > seems correct. I will try reading it into sybyl and then resave it into > another mol2 file. I am not familiar with that server. However, a Sybyl atom type for most atoms consists of the atomic symbol followed by a period followed by a number or a short character string. For example, C.3 is an sp3 hybridized carbon, N.ar is an aromatic ring nitrogen, and O.co2 is a carboxylic acid oxygen. I believe the file you have lacks the type designator after the atomic symbol for atom 1. > I am looking at making topology files for lipids like cardiolipin, di > myristoyl phosphatidylethanolamine, dimyristoyl phosphatidylinositol and > myristoleic acid. DO you know of any available gromacs topology files for > these? I cannot help you on that, but would suggest you ask those who have published lipid simulations. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 From: Sweta Iyer To: gmx-users@gromacs.org Sent: Sat, January 22, 2011 1:44:25 AM Subject: [gmx-users] Re: Problem with using topolbuild1_3.tgz > Date: Fri, 21 Jan 2011 06:55:30 -0800 (PST) > From: "Bruce D. Ray" > Subject: Re: [gmx-users] Problem with using topolbuild1_3.tgz > To: gmx-users@gromacs.org > Message-ID: <417950.70449...@web35801.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > On Thu, January 20, 2011 at 6:41PM, Sweta Iyer wrote: >> Hi, I am trying to generate topology files for a set of lipids with the >> help of topolbuild1_3.tgz package found at the other software page of >> GROMACS website. >> >> I downloaded and installed all files and tried running the program with >> a >> MOL2 file with charges in it. However, it shows an error message as >> follows: >> >> Fatal error. >> Source code file: readmol2.c, line: 758 >> Atom 1 (C) has 3 connections when allowed 0 >> >> I am not sure how to get over this problem! Wonder what will fix this >> error and get the program running! > > A major requirement of topolbuild is that the mol2 file use correct atom > types as defined by Tripos, whose file format mol2 is, and as used in > Sybyl. > The error message suggests that you have not specified correct Tripos > Sybyl > atom types. There may be other problems in your mol2 file as well. > Correct the atom types and check that the file is otherwise syntactically > correct and it should work. > > However, I believe that lipid topology files for gromacs are already > available > for download. > > I hope that helps. > > > -- > Bruce D. Ray, Ph.D. > Associate Scientist > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 Hi Bruce, Thanx for the reply. The MOL2 file was generated by the RESP ESP charge derive server. I did not check the file in SYBYL. However, structurally it seems correct. I will try reading it into sybyl and then resave it into another mol2 file. I am looking at making topology files for lipids like cardiolipin, di myristoyl phosphatidylethanolamine, dimyristoyl phosphatidylinositol and myristoleic acid. DO y
[gmx-users]Fwd: GROMACS and GBSA implicit water
On Wed, 26 Jan 2011 at 22:06:47 +0100 (CET), "battis...@libero.it" wrote: I am forwarding this to the Gromacs Users' list because that is the appropriate place for this. >excuse me if I am writing you directly. I read on gromacs web page your >advise about the implicit water, and I need to solve a problem for my phD work. While at my age I could easily have forgotten writing some off hand comment at some time, I do not recall that I ever gave any advice about implicit water. To the best of my knowledge, I have never used it. The only comment I can recall giving about water concerned not using -DFLEXIBLE in MD runs. >Can you help me about my problem? It is possible for you? anywhey very very >thanks! > >My problem: Your problem is an example of why all gromacs questions should be sent to the user's list rather than sending them privately. I absolutely do not have any clue why grompp does not pick up the gbsa.itp file you mention below, but I am sure somebody else might. >For my system I defined an atomtype in this way: >(I defined about 10 atoms type and for all I have got the same problem) > >[ atomtypes ] >; name bond_type mass charge ptype sigma(nm) epsilon(kj/mol) >NLAPT NC 14.0067 0.314 A 0.29760 0.87672 > > >if in the md.mdp file I set >; IMPLICIT SOLVENT ALGORITHM >implicit_solvent = no > >grompp tool give a good result, and mdrun can generate the good trajectories, >but if I use the implicit solvent : implicit_solvent = GBSA > >the tool grompp give the error: > >GB parameter(s) missing or negative for atom type 'NLAPT' > >Fatal error: >Can't do GB electrostatics; the implicit_genborn_params section of the >forcefield is missing parameters for 8 atomtypes or they might be negative. >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors > > >so I put the following parameter in the gbsa.itp file the parameter: > >[ implicit_genborn_params ] > >; atype sar st pi gbr hct >NLAPT 0.1551 1.0280.14880.79 ; N > > >but grompp give the error > >Couldn't find topology match for atomtype NLAPT >Aborted > > >Can you give me an idea in order to solve this problem? >Thank you very much!!! My idea is that you should keep all gromacs related correspondence on the gromacs users' e-mail list where somebody who actually knows something might see it. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Problem with using topolbuild1_3.tgz
On Thu, January 20, 2011 at 6:41PM, Sweta Iyer wrote: > Hi, I am trying to generate topology files for a set of lipids with the > help of topolbuild1_3.tgz package found at the other software page of > GROMACS website. > > I downloaded and installed all files and tried running the program with a > MOL2 file with charges in it. However, it shows an error message as > follows: > > Fatal error. > Source code file: readmol2.c, line: 758 > Atom 1 (C) has 3 connections when allowed 0 > > I am not sure how to get over this problem! Wonder what will fix this > error and get the program running! A major requirement of topolbuild is that the mol2 file use correct atom types as defined by Tripos, whose file format mol2 is, and as used in Sybyl. The error message suggests that you have not specified correct Tripos Sybyl atom types. There may be other problems in your mol2 file as well. Correct the atom types and check that the file is otherwise syntactically correct and it should work. However, I believe that lipid topology files for gromacs are already available for download. I hope that helps. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] topolbuild1_3 install problem
On Mon, December 27, 2010 at 5:02 AM, gromacs564 wrote: > Hi, Mark, > Thanks for the reply. > You'are right,I forgot to enter the path.And my computer system is Ubuntu >10.04.I want to use > the glycam force filed, then I type the command: > software/topolbuild1_3/src/topolbuild -h > I got the correct "help information". > But when I type this integral command: >software/topolbuild1_3/src/topolbuild -n myt -dir >software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename > > > it's error: > *...@ubuntu:~$ software/topolbuild1_3/src/topolbuild -n myt -dir >software/topolbuild1_3/dat/leap/parm -ff glycam06_c -r MAL -rename > Fatal error. > Source code file: atom_types.c, line: 87 > Cannot open file >software/topolbuild1_3/src/dat/parm/dat/antechamber/ATOMTYPE_GLYCAM.DEF > > > Do you know how to solve this problem ? > Thanks for you reply! The problem is that you are giving the wrong directory after -dir The -dir parameter entry is supposed to point to the directory that contains the dat directory because it needs the atom types file as well as the leap parameters file Try instead: software/topolbuild1_3/src/topolbuild -n myt -dir software/topolbuild1_3 -ff glycam06_c -r MAL -rename I hope this helps as well. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] topolbuild1_3 install problem
On Sun, December 26, 2010 at 6:07 AM, gromacs564 wrote: > I downloaded topolbuild1_3 from the GROMACS website, > and I run the command as follows: > > "path: home/buct/topolbuild1_3 ” > # tar -xvf topolbuild1_3.tgz > #make -f Makefile ; (intel CPU) there were no any error >messages. > then I write "export PATH=$PATH:/home/buct/topolbuild1_3 " into >etc/profile(root) > ``` > But When I type "topolbuild -h" I get "command not found",and I don't know > how >to deal it. > can anyone tell me to install the topolbuild1_3 correctly? First, I hope that you mean that you changed directory to home/buct/topolbuild1_3/src before giving the make command since Makefile is in src and not in the main directory which means that giving the make command in any other directory should give an error message. Second, the topolbuild binary will be in home/buct/topolbuild1_3/src after the build, but the commands you give search home/buct/topolbuild1_3 for an executable where there shouldn't be an executable. Third, the text files, in the main directory, home/buct/topolbuild1_3 do include installation and use information. Please see in particular INSTALLATION.txt and README.txt Fourth, the resulting topology from topolbuild 1.* works with gromacs 3.3.3 and gromacs 4.0.*, but the rearrangement of the force field files with gromacs 4.5.* means that the include file lines for such a topology will need minor editing with a text editor to be usable with gromacs 4.5.*One example of such editing has been posted. The 2.0 version of topolbuild will be designed for gromacs 4.5.*. I hope this helps you. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] topolbuild cannot open logfile
On Tue, September 28, 2010 at 7:38 PM, "andrew_m_nor...@talk21.com" wrote: > Hello i am very new to molecular mechanics so please excuse me if my > questions are a little naive or stupid. > I am trying to minimise a mol2 file with topolbuild1_3 using the following > command line arguments from within the topolbuild directory: > ./topolbuild -dir /usr/local/gromacs/share/gromacs/top -ff oplsaa >-n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move > > I get the following error: > > Fatal error. > Source code file: topolbuild.c, line: 345 > Cannot open log file zinc_12404782.log > > I realise that i will have to go over the parameters again but i was hoping >for some sort of output. > Does anyone know if it is a problem with the parameters of the input file >shown below or some > problem with the way in which topolbuild is called ? I am a little unsure > how >to point to the > oplsaa force fields? The problem with your command is that you do not have write permission in the directory in which topolbuild resides. You need to run the command from the directory in which you want the topology built with a command such as: /path-to-topolbuild-main-directory/src/topolbuild -dir /path-to-topolbuild-main-directory/dat/gromacs -ff oplsaa -n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move Note that the gromacs directory does not contain the topolbuild tables. Please see the examples given in the PROGRAM_TESTING_DONE.txt file in the topolbuild distribution for more information. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]
On Mon, August 23, 2010 12:12 PM, Eudes Fileti wrote: > Well, the line 40 is just one of the 36 parameters not found! > In this link ( https://sites.google.com/site/fileti/ ) I put > the complete files. > I know I need to determine which bond type should be called > and I believe that it has been done, but I don't know why > it's not being found. Well, I'm not Justin, but as I look at your topology, I see that you have a bond from atom 3, type CC322, to atom 6, also type CC322. However, when I look at the parameters you give in the bondtypes section, I cannot find a CC322 CC322 bond defined. Either the entry is missing or you did not post a complete set of force field entries. Missing entries might be the cause of theother parameters not found as well, which is what was suggested to you previously. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support
On Wed, March 10, 2010 at 3:35 PM, Joe Joe wrote: > This is great. I was able to easily make a molecule that runs with > OPLS-AA. Would it be possible to add a feature which creates an >*.rtp entry? It would be really useful for making non standard >amino acids and incorporating it with pdb2gmx. I've been working on something to do that. Because of some differences that require use of names given in defines, this would be a separate program from topolbuild despite sharing some component subroutines. Other research, plus my age tend to make this a slow process. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] On the new web site, how does one make a user contribution?
On Tue, March 9, 2010 at 8:30 PM, Rossen Apostolov wrote: > On 03/09/2010 09:15 PM, Bruce D. Ray wrote: >> I went to the new web site to make a user contribution, >> and I was not able to find the method to do that. >> In fact, I even had to create my user ID again that I >> had on the old web site. With this new web site, how >> does one go submitting user contributed software? >> > Hi Бруце, > > Many users who registered on the old wiki were given a default > status of "viewers" after the transition to the new site. I changed > your status and now you should be able to edit pages across the > site. Thank-you very much, both for the assistance and for rendering my name in Cyrillic. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] On the new web site, how does one make a user contribution?
On Tue, March 9, 2010 at 4:08, Justin A. Lemkul wrote: > Bruce D. Ray wrote: >> I went to the new web site to make a user contribution, >> and I was not able to find the method to do that. >> In fact, I even had to create my user ID again that I >> had on the old web site. With this new web site, how >> does one go submitting user contributed software? >> > You should be able to click "Attach file or image" on the > contributed software page, which will prompt a popup where > you select the file and write the description. That's what I thought, but at the time that was not working. Since the message from Rossen Spostolov, it is working. Thank-you very much. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support
. The van der Waals parameters are identical between the original rtp atom type and the topolbuild choice as well. When charges from the mol2 file rather than the oplsaa atom type charges are used, differences in atom type charges are moot. Thus, the effects of these changes are minimal.Curiously, the oplsaa atom type charges from the topolbuild atom type selections appear to be closer to the atom charges given in foplsaa.rtp than the atom type charges for the oplsaa types used in foplsaa.rtp I hope people find this version useful. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] On the new web site, how does one make a user contribution?
I went to the new web site to make a user contribution, and I was not able to find the method to do that. In fact, I even had to create my user ID again that I had on the old web site. With this new web site, how does one go submitting user contributed software? -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
On Sat, February 6, 2010 at 11:08:30 AM, Antoine Delmotte wrote: > Thank you very much for this, Bruce. It will help me, for sure. > > Could you just let me know where you found the parameters or how you generated them? Most of the parameters came from the entry for threonine in ffoplsaa.rtp The remainder came from running the most recent beta test version of topolbuild 1.3 with the command line /usr/local/bin/topolbuild -dir /usr/local/topolbuild -ff oplsaa -n tpo_pep -charge which generates an OPLSaa topology with parameters found originally in the Gromacs OPLSaa installation against a short peptide containing phosphothreonine and sets the atom charges to the OPLSaa atom type charges. I then edited the threonine entry from ffoplsaa.rtp according to add in the phosphate atom types, and change those atom types that are altered by the presence of the phosphate. Finally, I adjusted the charge on the phosphorous from the charge given in ffoplsaanb.itp in order to have the total charge come out as -2 for a fully ionized phosphate. The exact ionization would depend on pH, of course, and I would have to run the command for protonated TPO (TPH ? or TPH2 ? for the mono- and di-protonated species?) to further correct atom types and charges. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte wrote: > I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, > phosphothreonine), which Gromacs does not recognise. > > I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 > force field. However, I would like to use the OPLS-AA force field. I therefore need a topology > file for this force field, which cannot be provided by PRODRG (only useful for united atoms > force fields). > > Does anyone have an idea about where I could get the phosphothreonine itp > file for OPLS > force field? > > Otherwise, could someone give me clues or the link to a good tutorial about > how to create > this itp file myself? > > Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. > It also seems I am not the first one to have this problem but I could not find any solution on > the archive of the mailing list. The charges probably need a little more work, but this might be a start towards an rtp file for phosphothreonine to add to ffoplsaa.rtp. [ TPO ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_1580.205 2 HBopls_1400.060 2 OG1opls_447 -0.700 2 Popls_4451.795 3 O1Popls_446 -1.120 3 O2Popls_446 -1.120 3 O3Popls_446 -1.120 3 CG2opls_135 -0.180 4 HG21opls_1400.060 4 HG22opls_1400.060 4 HG23opls_1400.060 4 Copls_2350.500 5 Oopls_236 -0.500 5 [ bonds ] N H NCA CAHA CACB CA C CBHB CB OG1 CB CG2 OG1 P O1P P O2P P O3P P CG2 HG21 CG2 HG22 CG2 HG23 C O -C N [ dihedrals ] ; override some of the typebased dihedrals NCACB OG1dih_SER_THR_chi1_N_C_C_O CCACB OG1dih_SER_THR_chi1_CO_C_C_O CACB OG1 HG1dih_SER_THR_chi2_C_C_OH_HO [ impropers ] -CCA N Himproper_Z_N_X_Y CA+N C O improper_O_C_X_Y I hope that helps. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] topolbuild
On Tue, December 1, 2009 at 1:54:56 AM, Neha Bharat Gajaria wrote: > I have downloaded topolbuild1.2.1 but cannot extract files. Can anyone help > and check the link? Do you mean that gunzip topolbuild1_2_1.tgz | tar -xf - does not work for you? Also, please check the archives for some posted bug fixes for topolbuild1.2.1 Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] amber force field in gromacs
On Sat, November 21, 2009 at 2:36:08 AM, leila karami wrote: > I used amber03 force field in gromacs to study pr-dna interaction. > I compare my pdb file and ffamber03.rtp file. > I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1) > and C-terminal > (NUMBER 70) of my protein is GLY. > pdb file and rtp file relating to gly1 and gly70 are placed in follow. > pdb file of gly1: > 1 N NGLY 1 > 2 CA NGLY 1 > 3 C NGLY 1 > 4 O NGLY 1 > 5 1H NGLY 1 > 6 2HA NGLY 1 > 7 2H NGLY 1 > 8 3H NGLY 1 > 9 1HA NGLY 1 > rtp file of gly1: > [ NGLY ] > [ atoms ] > Namber99_39 0.29430 1 > H1amber99_17 0.16420 2 > H2amber99_17 0.16420 3 > H3amber99_17 0.16420 4 > CAamber99_11 -0.01000 5 > HA1amber99_28 0.08950 6 >HA2amber99_28 0.08950 7 > Camber99_20.61630 8 > Oamber99_41 -0.57220 9 I could be wrong, but I believe that the atom names in the pdb file are supposed to match the names in rtp entry. There may be some formatting issues as well in your actual pdb file since the error message references a residue GLY1 instead of residue NGLY1, but in the absence of the actual pdb entry line, I cannot comment on that. Sincerely -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Problem with topolbuild
On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson wrote: > Thank you. > I am new to Unix commands, so could you please explain a little more how I am > to > apply these bug fixes? For short patches like these, I just use a text editor. Because the mailing list does not like the length this would come to if I were to attach the edited files, I've sent a separate e-mail to you directly with the edited files for you to place in the topolbuild source directory and recompile. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Problem with topolbuild
On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson wrote: > I have a small organic molecule that I processed with antechamber using the gaff forcefield > and got a mol2 file. I want to get .gro and. itp files from this to use with GROMACS. So I tried > to use the program "topolbuild version 1.2" from the GROMACS website. > > when I execute the command: > "topolbuild -dir ../ -ff gaff -n nameofmolecule -r SL -last 1241 -resnum 40" > I get this error message: > Fatal error. > Source code file: readmol2.c, line: 109 > Atomic symbol cc in atom type not found. > > When I excecute the topolbuild above I use -dir ../ because that should take the program > to the directory containing dat/antechamber and etc. which actually comes with the > topolbuild 1.2 package > > I don't know what to do and I have tried searching this mailing list and > google without sucess. > > Can someone please help me? First, the mol2 file that you are using is not syntactically correct because it is using gaff atom types and not Tripos' Sybyl atom types. A syntactically correct mol2 file would not have atom type cc. Please process your organic molecule against the Sybyl force field to get a correct mol2 file. Second, there are a number of bug fixes I have placed in this list for version 1.2.1 which is the version I hope you are using. The following diffs should be applied: diff topolbuild1_2_1/src/Makefile topolbuild1_2_2/src/Makefile 22,23c22,29 < $(PROGRAM): $(SOURCES) < $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm --- > $(PROGRAM): $(OBJECTS) > $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm > > clean: > rm -f *.o > > dist_clean: > rm -f *.o $(PROGRAM) diff topolbuild1_2_1/src/Makefile.G4OsX topolbuild1_2_2/src/Makefile.G4OsX 22,23c22,29 < $(PROGRAM): $(SOURCES) < $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm --- > $(PROGRAM): $(OBJECTS) > $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm > > clean: > rm -f *.o > > dist_clean: > rm -f *.o $(PROGRAM) diff topolbuild1_2_1/src/ring_detect.c topolbuild1_2_2/src/ring_detect.c 450c450 <ar_set[(t_ring_atomno[i][j])][3]++; --- >ar_set[(t_ring_atomno[i][k])][3]++; diff topolbuild1_2_1/src/topolbuild.c topolbuild1_2_2/src/topolbuild.c 440c440 < max_rng = num_bonds/2; --- > max_rng = 3 * num_bonds/4; Also, when using Gromacs force fields, the defaults definition line needs to be changed from: 1 2 yes 0.5 0.8333 to: 1 1 no 1.0 1.0 Unfortunately, I did not allow for different defaults for different force fields in that version. The next version will correct that as well as adding OPLSAA to the suite of force fields available. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Fatal Equilibration Errors
On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy wrote: > In an earlier message, it was stated that topolbuild generated topologies with Gromos 53a6 > and OPLS-AA force fields. I am using topolbuild (version 1.2.2), and the only files in the > "dat/gromacs" directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. > How is the OPLS-AA force field used? First, I need to thank you in particular. First, while testing your molecules, I discovered a case in the as yet unreleased topolbuild 1.3 in which my dihedral selection method failed to select the dihedral choice with the maximum number of heavy atoms with OPLS-AA as the force field. Second, also because of this, I discovered what one downloads as a "Sybyl 2" structure from one source of small molecule structures and how to edit it so that it meets the syntax standards for a true mol2 file. Thank you very much for this assistance. In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2) generates topologies for amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. I stated that the as yet unreleased topolbuild 1.3 will include OPLS-AA. The version of topolbuild you have, is 1.2.2. Would you like to beta test topolbuild 1.3? Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Fatal Equilibration Errors
On Sunday, August 9, 2009 at 4:32:19 PM, Nancy wrote:
> I obtained the ethylene glycol (1,2-ethanediol) structure from the URL:
> http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb
>
> I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF
> Chimera (http://www.cgl.ucsf.edu/chimera/).
>
> I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the
> topologies:
>
> $ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir
> .../topolbuild1_2_2/dat/gromacs -ff gmx53a6
>
> which outputs the files:
>
> ethanediol.gro
> ethanediol.log
> ethanediolMOL.mol2
> ethanediol.top
> ffethanediol.itp
> posreethanediol.itp
>
> I modified the "ffethanediol.itp" file to read:
>
> ===
> #define _FF_GROMOS96
> #define _FF_GROMOS53A6
> #define _FF_USER
>
> [ defaults ]
> ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 1 no 1.0 1.0
>
> #include "ffG53a6nb.itp"
> ===
>
> The
lack of hydrogen bonds between the solute and solvent molecules was
> due
to the lack of charges in the generated topology file
"ethanediol.top".
> So I changed the "atoms" section of the topology
file (the original topology
> file is at the end of this message), and
this causes hydrogen bonds between the
> solute and solvent in numbers
comparable to that between the solvent molecules.
>
> ===
> [ atoms ]
> ; nrtype resnr residu atom cgnrcharge mass
> 1 CH2 1 EDO C11 0.17600 14.02700 ;
> 0.000
> 2OA 1 EDO O11 -0.5740 15.99940 ;
> 0.000
> 3H 1 EDO HO11 0.39800 1.00800 ;
> 0.000
> 4 CH2 1 EDO C22 0.17600 14.02700 ;
> 0.000
> 5OA 1 EDO O22 -0.5740 15.99940 ;
> 0.000
> 6H 1 EDO HO22 0.39800 1.00800 ;
> 0.000
> ; total molecule charge = 0.000
> ===
>
> I
obtained the charge values from the methanol tutoral included with
Gromacs
> (.../share/gromacs/tutor/methanol/methanol.itp). I then
enlarge the box and solvate the molecule:
I used a mol2 file that I generated from a sy2 file downloaded from NCI by first
running the file through dos2unix then replacing the 0 in the residue number
column with 1 EDO so that I had both a correct residue number column with a
residue name column. The NCI data was missing the residue name column. I then
read the mol2 file that resulted into UCSF Chimera and used it to generate
gasteiger
charges for ethylene glycol. Chimera wrote the following mol2 file as a result:
@MOLECULE
EDO
10 9 1 0 0
SMALL
AMBER99
@ATOM
1 O1 0.0.0. O.3 1 EDO-0.3940
2 C1 -0.9400 -0.1600 -1.0400 C.3 1 EDO 0.0662
3 C2 -1.74001.1400 -1.1400 C.3 1 EDO 0.0662
4 O2 -2.52001.28000.0200 O.3 1 EDO-0.3940
5 H1 0.5196 -0.80240.0879 H 1 EDO 0.2102
6 H2 -1.5882 -0.9871 -0.8384 H 1 EDO 0.0588
7 H3 -0.4343 -0.3499 -1.9636 H 1 EDO 0.0588
8 H4 -2.37211.1133 -2.0029 H 1 EDO 0.0588
9 H5 -1.06961.9696 -1.2252 H 1 EDO 0.0588
10 H6 -3.02712.0935 -0.0316 H 1 EDO 0.2102
@BOND
115 1
212 1
327 1
426 1
523 1
639 1
738 1
834 1
94 10 1
@SUBSTRUCTURE
1 EDO 2 RESIDUE 4 A EDO 0 ROOT
I processed this with topolbuild 1.3 and generated topologies with gromacs
53a6 and with opls-aa as the force fields. I am attaching the results to this
as the tarred and gzipped file, ethanediol.tgz I note that the opls-aa atom
types selected by topolbuld 1.3 have characteristic atom type charges charges
of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to oxygens,
+0.06 for each of the hydrogens bound to carbon, and +0.145 for each of the
carbons. The comparison to the gasteiger charges Chimera assigned to these
atoms is interesting. The opls-aa topology generated also assigns to the
O1-C1-C2-O2 dihedral the diol constants found as a special define in
ffoplsaabon.itp
{snipped}
> The ethylene glycol lacks explicit non-polar hydrogens; is that
normal for this type of system,
> force field (based on GROMOS96
Re: [gmx-users] Energy Minimisation and Equilibration Problems
On Thursday, August 6, 2009 at 7:59:43 PM Nancy wrote: > I ran the minimisation, and mdrun gave the following last few lines of output: > > == > Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom= 2395 > Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom= 2395 > Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom= 2395 > Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom= 2395 > Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom= 2395 > Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom= 2395 > Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom= 2395 > Step=1, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom= 2395 > Step=2, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom= 2395 > > writing lowest energy coordinates. > > Steepest Descents did not converge to Fmax < 10 in 20001 steps. > Potential Energy = -7.1493609e+04 > Maximum force = 2.4185994e+04 on atom 2395 > Norm of force = 8.1511212e+02 > == > > As you can be seen, the forces still do not converge to Fmax < 10, even after > 20,000 steps. > > Does anyone know what the problem might be? The problem is my error in the specification of non-bonded interaction combination rules, FudgeLJ, and FudgeQQ for gromacs force fields. Line 7 of your file ffethanediol.itp currently reads: 1 2yes 0.5 0.83 This was taken from ambconv and is correct for amber and gaff force fields, but not for gromacs force fields, nor for OPLS-AA. Change line 7 of the file ffethanediol.itp to read: 1 1 no 1.0 1.0 The correction is in topolbuild 1.3 which is not yet released, but this error was not caught for the topolbuild 1.2 series. Quite frankly, I had forgotten that modification was made as I've been editing the set of tables needed to add OPLS-AA to the mix of force fields available. As a general note. For gromacs force field topologies generated with anything in the topolbuild 1.2 series, this edit to the itp file that specifies the defaults is required. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Energy Minimisation and Equilibration Problems
uild1_3 -dir /usr/bdray/tables -ff gmx53a6 -n glycol/ethylene_glycol editconf -f ethylene_glycol.gro -o ethanediol_box.gro -box 3 3 3 -c genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_solv.gro -p ethanediol.top -box 3 3 3 grompp -f em.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr File em.mdp includes: constraints = none integrator = steep nsteps = 2 ; ;Energy minimizing stuff ; emtol = 10.0 emstep = 0.01 nstlist = 1 coulombtype = PME nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.3 nstxout = 1 pbc = xyz pme_order = 4 I deliberately did not use the flexible waters model with this energy minimization I then ran mdrun -v -deffnm em I got the result: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 6291 steps, but did not reach the requested Fmax < 10. Potential Energy = -4.9487391e+04 Maximum force = 9.0675652e+01 on atom 5 Norm of force = 2.5599347e+02 I note that atom 5 is part of the ethylene glycol molecule. Furthermore, with very few exceptions, most of the activity in the energy minimization was devoted to the ethylene glycol molecule. I presume that I would reach the desired Fmax if I were to use double precision. However, an Fmax < 90.7 would seem to me to be usable. Perhaps the problem stems from the use of flexible waters in the energy minimization? -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Energy Minimisation and Equilibration Problems
On Thursday, August 6, 2009 at 11:58:20 AM, Nancy wrote: > The energies simply do not seem to come down any further within several > thousand steps. > > I start with a .mol2 file which contains the structure of ethylene glycol (ethanediol). > These are the commands that I use to set up and run the minimisation: > > $ .../topolbuild1_2_1/src/topolbuild -n ethanediol -dir > .../topolbuild1_2_1/dat/gromacs -ff gmx53a6 > > the above command outputs the following files: > > ethanediol.gro > ethanediol.log > ethanediolMOL.mol2 > ethanediol.top > ffethanediol.itp > posreethanediol.itp Those are the correct files to be generated for the topolbuild command given. Are the parameters blank in any of the lines in ethanediol.top? Are there any lines in ethanediol.log that do not involve nonpolar hydrogens that have asterisks instead of parameter values? > I then proceed to enlarge the box and solvate the molecule: > > $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5 > > $ genbox -cp ethanediol_box.gro -cs spc216.gro -o ethanediol_box.gro -p > ethanediol.top -shell 1 Is this a shell of solvent around the molecule rather than a box of solvent containing the molecule of interest? How is that to work with vacuum outside the shell? > I then use grompp to configure the minimisation: > > $ grompp -f minim.mdp -c ethanediol_box.gro -p ethanediol.top -o em.tpr > > This is my .mdp file for minimisation: > > === > define= -DPOSRE Why position restraints when doing energy minimization? > integrator= steep > emtol= 10.0 > emstep = 0.01 > nsteps= 2000 Why so few steps when the emtol is this small. For this emtol, I would expect to need 1 to 2 steps. > nstlist= 1 > ns_type= grid > rlist= 1.0 > coulombtype= PME > rcoulomb= 1.0 > rvdw= 1.3 > pbc= xyz > > pme_order= 4 > constraints = none > > > nstxout= 1 > nstvout= 1 > nstenergy= 1 > nstlog= 1 > nstcomm = 1 > Tcoupl = no > Pcoupl = no > gen_vel = no > === I've been told that the last three lines are not needed for energy minimization. > $ mdrun -v -deffnm em > > the minimisation runs without error and these are the last few lines of > output: > > === > Step= 1990, Dmax= 1.1e-05 nm, Epot= -1.76427e+04 Fmax= 1.25524e+04, atom= 304 > Step= 1991, Dmax= 1.3e-05 nm, Epot= -1.76433e+04 Fmax= 3.13881e+04, atom= 484 > Step= 1992, Dmax= 1.6e-05 nm, Epot= -1.76443e+04 Fmax= 2.11785e+04, atom= 484 > Step= 1993, Dmax= 1.9e-05 nm, Epot= -1.76445e+04 Fmax= 4.22489e+04, atom= 484 > Step= 1994, Dmax= 2.3e-05 nm, Epot= -1.76456e+04 Fmax= 3.33021e+04, atom= 484 > Step= 1996, Dmax= 1.4e-05 nm, Epot= -1.76468e+04 Fmax= 1.26110e+04, atom= 304 > Step= 1997, Dmax= 1.6e-05 nm, Epot= -1.76474e+04 Fmax= 3.81619e+04, atom= 484 > Step= 1998, Dmax= 2.0e-05 nm, Epot= -1.76486e+04 Fmax= 2.68240e+04, atom= 484 > Step= 2000, Dmax= 1.2e-05 nm, Epot= -1.76496e+04 Fmax= 1.26501e+04, atom= 304 > > writing lowest energy coordinates. > > Steepest Descents did not converge to Fmax < 10 in 2001 steps. > Potential Energy = -1.7649566e+04 > Maximum force = 1.2650057e+04 on atom 30 > Norm of force = 1.7544460e+03 > === > > If I proceed to equilibration after doing the above, the water molecules simply fly apart > (although not immediately). Additionally, it seems that there are no interactions between > the waters during equilibration. Really no point in proceeding further until the energy minimization issues are solved. > I have tried to run the minimisation for a larger number of steps, but it does not help. > I have also tried to delete individual water molecules from the structure files, but doing > so simply causes the minimisation to "fixate" on another two molecules. I am not sure > what values of the energies are reasonable for this system, and how to minimise it further. > Please advise. I've never used the -shell with genbox and don't know what effect that would have on energy minimization. -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Energy Minimisation and Equilibration Problems
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy wrote:
> I am trying to run equilibration on my solvated ethylene glycol
(ethanediol) system. I started
> with an ethanediol mol2 file from which
topolbuild generated various files. I used editconf
> to enlarge to box
of the "ethanediol.gro" file:
>
> $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
>
> and then I used genbox to solvate it:
>
> $ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o
> ethanediol_solv.gro -p ethanediol.top
>
>
I ran energy minimisation on it:
>
> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
>
> my minim.mdp file is:
>
> ==
> define= -DFLEXIBLE
> integrator= steep
>
emtol= 1000.0
> emstep = 0.01
> nsteps= 5000
>
> nstlist= 1
> ns_type= grid
> rlist= 1.0
> coulombtype= PME
> rcoulomb= 1.0
> rvdw= 1.3
> pbc= xyz
>
> pme_order= 4
> constraints = none
>
> nstxout= 1
> nstvout= 1
> nstenergy= 1
> nstlog= 1
> ==
>
> $ mdrun -v -deffnm em
>
> and the energies converge (although I think that the values are still too
> large for this system):
>
> ==
> Steepest Descents converged to Fmax < 1000 in 12 steps
> Potential Energy = -1.1206108e+04
> Maximum force = 9.4016180e+02 on atom 31
> Norm of force = 3.4989252e+02
> ==
{remainder snipped}
The energies do seem large. What happens if you do energy minimization
with emtol = 10.0 ?
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
>
>From: Nancy
>To: Discussion list for GROMACS users
>Sent: Wednesday, August 5, 2009 10:28:47 PM
>Subject: [gmx-users] Energy Minimisation and Equilibration Problems
>
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Re: [gmx-users] Energy Minimisation Values
On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy wrote: > I was trying to run equilibration on my solvated ethylene glycol system. However, the > system seems to be "exploding". I believe this is due to inadequate energy minimisation, > however, I am unable to minimise my system any further. I am using the following .mdp > file "minim.mdp" for minimsation: > > == > define= -DFLEXIBLE > integrator= steep > emtol= 1000.0 > emstep = 0.5 > nsteps= 1000 I use more steps than 1000 (may want 1) with: emstep = 0.01 nstcomm= 1 Tcoupl = no Pcoupl = no gen_vel = no > > nstlist= 1 > ns_type= grid > rlist= 1.0 > coulombtype= PME > rcoulomb= 1.0 > rvdw= 1.3 > pbc= xyz > > pme_order= 4 > constraints = none > == > > I process it with grompp, where "ethanediol_solv.gro" is the solvated system, > and "ethanediol.top" is the topolgy generated with topolbuild: > > $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr > > I then run it: > > $ mdrun -v -deffnm em > > mdrun outputs the following information: > > == > Steepest Descents did not converge to Fmax < 1000 in 1001 steps. > Potential Energy = -6.7546914e+03 > Maximum force = 2.7262363e+04 on atom 34 > Norm of force = 2.5032930e+03 > == > > I have viewed the output trajectory of the minimisation and I can see that the > waters do not move much. I am wondering if there is a way to let solvent water > molecules move about during minimsation, and/or how to remove some of them. > I am also unsure what value of emtol is reasonable for this type of small system. I use the same value of emtol, but that's just based on examples I've seen where others have used that value. -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 > >From: Nancy >To: Discussion list for GROMACS users >Sent: Wednesday, August 5, 2009 6:03:51 PM >Subject: [gmx-users] Energy Minimisation Values > > > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] Re: MD Simulation Errors for Ethylene Glycol-Water System
nt length > 1 4 88.80.6606 0.6855 0.1520 > 2 3 90.60.4305 0.4542 0.1000 > 1 2 89.20.6123 0.4690 0.1435 > 5 6 93.40.4193 0.1741 0.1000 > 4 5 89.20.6156 0.5033 0.1435 > === > It is blowing up. Did you see anything in the energy minimization or the position restrained equilibration steps that seemed unusual? > > I am not sure where the errors are occuring (I am also wondering if the absence of > explicit non-polar hydrogens in the .gro files are relevant). Please adivse. Gromacs force fields are united atom force fields. As such, explicit non-polar hydrogens are supposed to be removed. I hope these few remarks help. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Carbohydrate MD Simulation
On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy wrote: > If it necessary to manually create force field parameters for each molecule, then how can one run a > simulation involving a number of arbitrary molecules (e.g. a set of mono and disaccharides) for > which there are no existing force fields? > > Do you know of any other MD software package that is capable of running simulations on > arbitrary molecules without having to "piece together" a force field for each molecule? Provided that the desired force field has suitable parameters for a particular bonding situation already, there are software packages that can generate a potentially suitable topology from a molecule's structure. For gromacs topologies, user contributions to gromacs include topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields (my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions is ambconv that takes the file generated by antechamber and leap from amber tools and generates a gromacs topology that uses the amber or gaff forcefield selected when leap was applied to the antechamber output. Another option is the Perl script mktop at <http://labmm.iq.ufrj.br/mktop/>, documented in Ribeiro, A.A.S.T., Horta, B.A.C., and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also there is acpypi, the AnteChamber Python Parser Interface available at <http://code.google.com/p/acpypi/>. I hope one of these with careful selection of the force field will be helpful to you. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] problem with installation of topolbuild1.2.1
On Wednesday, July 8, 2009 2:32:53 AMsubarna thakur wrote: > Can anybody please tell me how to install topolbuild 1.2.1 programm in 32 bit machine with > Fedora linux operating system. I cannot understand the instruction given in the READ ME file Apparently some versions of make do not handle my make files the same way that the version of make I use does. to correct this, replace the file in src named Makefile with the attached version. Second, to allow larger memory allocation for recursive ring detection in some complicated ring systems, the estimate of maximum number of rings needs to be increased. In the source code, in file topolbuild.c, change the following line: max_rng = num_bonds/2; to max_rng = 3 * num_bonds/4; Third, to correct for an error in setting a ring type flag, in file ringdetect.c, function aromaticity change ar_set[(t_ring_atomno[i][j])][3]++; to ar_set[(t_ring_atomno[i][k])][3]++; Then type make to compile. Once the program is compiled, you can relocate the executable, named topolbuild, and the entire dat directory where you wish them to be. Items in the water_and_ions directory need to be placed where grompp can find them. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 Makefile Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Installing topolbuild
04.2670 -0.1900 H 1 UNK10.2548
39 H 3.81501.95007.5800 H 1 UNK10.0654
40 H 1.74505.65106.6810 H 1 UNK10.0654
41 H 4.33602.75609.7690 H 1 UNK10.0630
42 H 2.33706.48508.9220 H 1 UNK10.0630
@BOND
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2 2 41
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4 3161
5 3171
6 4 91
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8 5 91
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341718 ar
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361820 ar
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42 2122 ar
4321421
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--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
___
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Re: [gmx-users] Installing topolbuild
Apparently some versions of make do not handle my make files the same way that the version of make I use does. The attached Makefile might help in such cases. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 Makefile Description: Binary data ___ gmx-users mailing listgmx-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
Re: [gmx-users] Installing topolbuild
From: vivek sharma To: Discussion list for GROMACS users Sent: Subject: Re: [gmx-users] Installing topolbuild On Friday, March 6, 2009 2:29:32 AM, vivek sharma wrote: > Thanks for your reply. I am workin on RHEL with architecture x86_64. > when i searched for libm.* I got a few location, I tried "make: again after > exporting these location in LD_LIBRARY_PATH. but i am getting the > same error again. I am not familiar with RHEL nor with x86_64 bit architecture. I believe that 64 bit *nixes have both 32 bit and 64 bit libraries. Thus, one needs to select the correct libm.* for the compilation options. It is probably best to use 32 bit compilation options for topolbuild, but I don't know what those would be for the compiler you are using. > I think, i didn't downloaded the appropriate files for > installation. Can you tell me the appropriate location to download the > topolbuild. topolbuild 1.2.1 (does gromacs ua and amber forcefields) is at: <http://www.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/> topolbuild 1.1.2 (does amber forcefields only) is at: <http://www.gromacs.org/component/option,com_docman/task,doc_download/gid,84/Itemid,26/> > And some precise installation instruction can help me more, as I am not > comfortable with linux env. Because I do not know every system and in particular have absolutely no knowledge of RHEL in general or RHEL with architecture x86_64 in particular, the only instructions I can give you are: 1. Set appropriate environmental parameters for your system. 2. Edit one of the two Makefiles (Makefile and Makefile.G4OsX) supplied to set such parameters as compiler, compilation options, library selections, and needed libraries appropriate for your system. 3. make -f Both Makefile and Makefile.G4OsX specify the compiler with the line CC = cc This might need to be changed either by passing the option when invoking make or by editing the appropriate file. Compiler options are the only line that differs between Makefile and Makefile.G4OsX and are specified on a line that reads for Makefile: CFLAGS = -O or for Makefile.G4OsX: CFLAGS = -O2 -mcpu=7450 -mtune=970 The compilation instruction reads: \t$(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm where I am denoting the tab at the start of the line with "\t" because this composer seems to replace the tab with spaces and I want this to be absolutely clear. Pointers to special libraries can be added to this line as -L/. Libraries are selected with -l. All of the systems to which I have ever had access have always had exp and sqrt functions located in /usr/lib/libm.so (SUN), /usr/lib32/libm.so (SGI), or /usr/lib/libm.dylib (Os X). You should check your systems documentation to be sure that the correct library and correct library options are selected. I do not have access to very many systems. This has compiled on Mac G4 ppc simply by typing -f Makefile.G4OsX I am told that it compiles on intel based Mac's running OsX and on at least some versions of 32 bit Linux. As I look at your error message, it appears to me as if there might have been some prior warning messages that could shed more light on this. In particular, where is math.h located? > 2009/3/5 Bruce D. Ray > On Thursday, March 5, 2009 1:47:28 AM, > vivek sharma wrote: >> I am trying to Install topolbuild on my system, while doing so with >> the make file given in the topolbuild folder. but I end up with a list >> of error mentioned below: >> .. >> . >> . >> . >> .compare_FF.c:(.text+0x1285): undefined reference to `exp' >> compare_FF.c:(.text+0x12cc): undefined reference to `sqrt' >> collect2: ld returned 1 exit status >> make: *** [topolbuild] Error 1 >> >> If somebody has tried this. please help me in figuring out the problem. > > The errors mean that ld cannot locate the math library ( the -lm in the > compilation instruction in Makefile which tells it to link against libm.* > that is usually found in /usr/lib . On most *nix's, this is libm.so but > its libm.dylib on Mac OS X.) If libm.* is not present in either the > standard location, or in someplace pointed to by LD_LIBRARY_PATH > then it will not be found. > > What is the system on which you are trying to build, where is libm.* > located, and what is LD_LIBRARY_PATH set to? If libm.* is in > some unusual place, then the easiest way to go is to add that location > to LD_LIBRARY_PATH > > As a side note, an early version of topolbuild was missing the -lm > in the compilation instruction in Makefile. I checked what I've > submitted since then and the makefiles all have the -lm as the last > item in the compilation instruction. Sincerely, -- Bruce D. Ray, Ph.D
Re: [gmx-users] Installing topolbuild
On Thursday, March 5, 2009 1:47:28 AM, vivek sharma wrote: > I am trying to Install topolbuild on my system, while doing so with > the make file given in the topolbuild folder. but I end up with a list > of error mentioned below: > .. > . > . > . > .compare_FF.c:(.text+0x1285): undefined reference to `exp' > compare_FF.c:(.text+0x12cc): undefined reference to `sqrt' > collect2: ld returned 1 exit status > make: *** [topolbuild] Error 1 > > If somebody has tried this. please help me in figuring out the problem. The errors mean that ld cannot locate the math library ( the -lm in the compilation instruction in Makefile which tells it to link against libm.* that is usually found in /usr/lib . On most *nix's, this is libm.so but its libm.dylib on Mac OS X.) If libm.* is not present in either the standard location, or in someplace pointed to by LD_LIBRARY_PATH then it will not be found. What is the system on which you are trying to build, where is libm.* located, and what is LD_LIBRARY_PATH set to? If libm.* is in some unusuall place, then the easiest way to go is to add that location to LD_LIBRARY_PATH As a side note, an early version of topolbuild was missing the -lm in the compilation instruction in Makefile. I checked what I've submitted since then and the makefiles all have the -lm as the last item in the compilation instruction. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-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
Re: [gmx-users] OPLS-AA topologies for ATP/ADP.
On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela wrote: > Does anybody have the topology files for ATP and/or ADP for the OPLS-AA > forcefield?. If not, how can I parameterize this molecules?. > Best regards. >Lucio Montero. > > Lucio Ricardo Montero Valenzuela > Instituto de Biotecnologia, UNAM > Departamento de Biologia Molecular de Plantas > Av. Universidad 2001, Col. Chamilpa > Cuernavaca 62210 > Mexico I've not tested this at all, but from my attempts to add OPLS-AA to topolbuild, I get the following that might be suitable for insertion in the oplsaa rtp: [ ATP ] [ atoms ] O9Popls_441 -0.635 0 ;O2 O8Popls_441 -0.635 1 ;O2 O7Popls_441 -0.635 2 ;O2 PGopls_445 0.072 3 ;P O6Popls_442 -0.286 4 ;OS O5Popls_441 -0.516 5 ;O2 O4Popls_441 -0.516 6 ;O2 PBopls_440 0.280 7 ;P O3Popls_442 -0.250 8 ;OS O2Popls_441 -0.516 9 ;O2 O1Popls_441 -0.51610 ;O2 PAopls_440 0.27611 ;P O5*opls_442 -0.31512 ;OS C5*opls_443 0.08513 ;CT H5*1opls_444 0.05914 ;HC H5*2opls_444 0.05915 ;HC C4*opls_174 0.11316 ;CT H4*opls_176 0.06517 ;HC O4*opls_186 -0.34818 ;OS C1*opls_193 0.16019 ;CO H1*opls_194 0.08420 ;HC N9opls_354B -0.24521 ;NA C8opls_353 0.09222 ;CK H8opls_359 0.10023 ;H5 N7opls_352 -0.23324 ;NB C5opls_350 0.14525 ;CB C6opls_351 0.14726 ;CA N6opls_356 -0.34127 ;N2 H61opls_357 0.14428 ;H H62opls_358 0.14429 ;H N1opls_346 -0.21930 ;NC C2opls_347 0.12031 ;CQ H2opls_355 0.06632 ;H5 N3opls_348 -0.21833 ;NC C4opls_349 0.15934 ;CB C2*opls_174 0.12735 ;CT H2*opls_176 0.10036 ;HC O2'opls_171 -0.38537 ;OH H2'opls_172 0.21038 ;HO C3*opls_174 0.11339 ;CT H3*opls_176 0.06540 ;HC O3'opls_171 -0.38641 ;OH H3'opls_172 0.21042 ;HO [ bonds ] PG O9P PG O8P PG O7P O6PPG PB O6P PB O5P PB O4P O3PPB PA O3P PA O2P PA O1P PA O5* O5* C5* C5* C4* C5* H5*1 C5* H5*2 C4* O4* C4* H4* C4* C3* O4* C1* C1*N9 C1* H1* C1* C2* N9C8 C8H8 C8N7 N7C5 C5C6 C5C4 C6N6 N6 H61 N6 H62 C6N1 N1C2 C2H2 C2N3 N3C4 C4N9 C2* C3* C2* H2* C2* O2' O2' H2' C3* H3* C3* O3' O3' H3' Please let me know if this actually works for computations. Charges were derived from the .mol2 file generated by Sybyl. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-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
[gmx-users] topolbuild 1.2.1, gromacs topology builder for gromacs and amber force field topologies
I have submitted a further revision of topolbuild as file topolbuild1_2_1.tgz This should work much better than the previous release that was rushed on account of personal factors that threatened to preclude further work. topolbuild 1.2.1 Reads a Tripos .mol2 file with charges to generate something approximating gromacs *.gro, *.top, and *.itp files from it based on selected force field parameters. Now supports some united atom force fields. Includes tables to support amber, gaff, glycam, and gmx type force fields. Requires that the *.mol2 file have syntactically correct Tripos atom types and absolutely will not work with other input atom types. Includes capability of pruning dihedral angles to a possibly more reasonable set. Revisions include: 1. Corrected errors in prior version from last minute additions. 2. Corrected output of defines and includes. 3. Refined the gromacs force field tables. 4. Revised log and topology outputs to better reflect the types of dihedrals. 5. Updated parameter files for gaff, glycam, and amber to the versions found in AmberTools 1.2 6. Revised order of setting dihedrals to better reflect tleap or grommp settings. 7. Improved option to prune excess dihedral angles. Most users should be satisfied with the results from setting -purge 1 8. Improper dihedrals generated for amber, glycam, gaff, and Tripos force fields are now included with regular type 1 dihedrals in accordance with the way that amber treats improper dihedrals. 9. Ion type names for the amber force fields now written in the topology as atomic symbol with charge to differentiate from other atom types in some force fields. Special Processing Used for Gromacs Force Fields Gromacs force fields have a limited set of atom types that are used in multiple chemical environments. This works quite well when one can use a residue types file to generate a topology. This presents problems when the goal is to determine the topology of an arbitrary molecule for which residue type information does not exist. Therefore, conversion to gromacs force fields requires double determination of atom types. A first determination of atom types is performed with a rich set of atom types derived from a combination of the gaff and amber atom type definitions. This assignment is used to determine force constants, bond lengths, angles, dihedral angles, and improper angles. A second determination of atom types is performed to assign the true gromacs atom types to match the atom types in the appropriate ffGnb.itp from the gromacs distribution. A major problem of this double conversion is that for something found in a residue type file, topolbuild does not always select the exact same parameters as are found in the residue type file’s parameterization. However, tests so far give the same parameterization better than 95% of the time. As always, I hope people find this useful. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-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
[gmx-users] topolbuild 1.2, gromacs topology builder extended to include gromacs united atoms force fields
I have submitted a further revision of topolbuild as file topolbuild1_2.tgz Please see the end of this message for an important post-submission code correction. Reads a Tripos .mol2 file with charges to generate something approximating gromacs .gro, .top, and .itp files from it based on selected force field parameters. Now includes some support for united atom force fields. Includes tables to support amber, gaff, glycam, and gmx type force fields. Requires that the .mol2 file have syntactically correct Tripos atom types and absolutely will not work with other input atom types. Includes capability of pruning dihedral angles to a possibly more reasonable set. Revisions include: 1. Corrected improper dihedrals determination. 2. Added gromacs united atoms force fields, along with some required atom type definition files and parameters files. Atom type definition files and parameter files are included for gmx43a1, gmx43a2, gmx43b1, gmx45a3, gmx53a5, and gmx53a6. Only the table for gmx53a6 has received any checking. All of these tables are incomplete and to be considered experimental. As with any automatic system for parameterization, careful examination and editing of the results is required to generate a well behaved final topology. 3. Added glycam force fields option and ATOMTYPE_GLYCAM.DEF. The glycam option is experimental and may not give a correct result. 4. Added option to prune excess dihedral angles. 5. Added conversion of some ring planarity dihedral angles to be output in the topology as improper dihedral angles. 6. Added an internal adjustment to correct for the problem of programs other than Sybyl generating larger charges than those from the standard Sybyl residue dictionary and charge generation methods. 7. Altered topology outputs to allow for various types of bond, angle, and dihedral angle parameters. 8. Made changes to antechamber data tables to correct for problems related to gromacs case insensitivity and for the absence of some atom type combinations in the force field parameters. Special Processing Used for Gromacs Force Fields Gromacs force fields have a limited set of atom types that are used in multiple chemical environments. This works quite well when one can use a residue types file to generate a topology. This presents problems when the goal is to determine the topology of an arbitrary molecule for which residue type information does not exist. Therefore, conversion to gromacs force fields requires double determination of atom types. A first determination of atom types is performed with a rich set of atom types derived from a combination of the gaff and amber atom type definitions. This assignment is used to determine force constants, bond lengths, angles, dihedral angles, and improper angles. A second determination of atom types is performed to assign the true gromacs atom types to match the atom types in the appropriate ffGnb.itp from the gromacs distribution. A major problem of this double conversion is that for something found in a residue type file, topolbuild does not always select the exact same parameters as are found in the residue type file’s parameterization. However, tests so far give the same parameterization better than 95% of the time. Post-submission code correction: I discovered that code in the file improper.c did not generate united atom model improper dihedral angles for tetrahedral carbons with a single attached proton. To correct this, please replace files in topolbuild1_2/src with the attached files. Once again, I hope people find this useful. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 corrections.tgz Description: application/compressed-tar ___ gmx-users mailing listgmx-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] topolbuild 1.1.2, further revisions to an all-atoms model gromacs topology generator
I have submitted a further revision of topolbuild as file topolbuild1_1_2.tgz that has the ability to use the new antechamber tables included with AmberTools 1.0. This version incorporates the following changes: 1. Changed maximum atom types allowed to permit use of the new version of ATOMTYPE_GFF.DEF distributed with AmberTools 1.0. 2. Improved determination of improper dihedrals. 3. Corrected atom type determination to set and to check for plain type AB bonds. 4. Made cosmetic corrections to log file output. 5. Included a gaff.dat file modified from the one distributed with AmberTools 1.0 to add atom type cz entries for mass and polarizability, for improper dihedrals, and for van Der Waals interactions. 6. Replaced the ATOMTYPE_GFF.DEF file with one derived from the ATOMTYPE_GFF.DEF distributed with AmberTools 1.0. Once again, I hope people find this useful. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-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] topolbuild 1.1.1, minor revisions to an all-atoms model gromacs topology generator
I have submitted a minor revision of topolbuild that I hope is more portable. Version 1.1.1 is now available in the user contributions at the gromacs web site. The following revisions have been made: 1. Removed all non-pointer references to NULL. 2. Gave all external variables single defining declarations with initializations all set in the file initializations.c 3. Corrected problem with carbonyls and some nitrogens when correcting for charges in atom type assignment. 4. Altered atom ordering to put H's with their parent atoms. 5. Added parameterization for the C -CT-NT angle in amber99 force field. This parameterization is missing in amber99 and presumably in other editions of the amber force fields as well. Curiously, the equivalent parameterization is present in gaff. 6. Divided force field output routines to better allow for addition of other force field output requirements. 7. Added an attempt at dihedral restraints output in the topology. 8. Changed the defines required for restraints. 9. Arranged for all output to go to the current directory when the input .mol2 file is in another directory. The parameter to the -n includes a directory path in such cases and the path is stripped from the names of the output files. As with the original, the required input is a syntactically correct mol2 file with Tripos atom types. At this time, output is still limited to topologies with amber, gaff, or Tripos force fields. I hope this proves useful. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-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
