Re: [gmx-users] AMBER to GROMACS conversion

e 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. Indiana

Re: [gmx-users] Topolbuild configuration

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 t

Re: [gmx-users] topolbuild and charges

ome 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.  

[gmx-users] Re: Thanks for your help!

phisticated 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 acce

[gmx-users] Re: topolbuild1_3:Illegal characters for size information line in mol2 file.

polbuild. 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-use

Re: [gmx-users] Regarding generating topology file.

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_L

Re: [gmx-users] use AMBER ff03 force field in gromacs 4

ncludes 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

Re: [gmx-users] Re: Problem with using topolbuild1_3.tgz

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 ava

[gmx-users]Fwd: GROMACS and GBSA implicit water

ted > > >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,

Re: [gmx-users] Problem with using topolbuild1_3.tgz

e 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 Scienti

Re: [gmx-users] topolbuild1_3 install problem

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 we

Re: [gmx-users] topolbuild1_3 install problem

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

Re: [gmx-users] topolbuild cannot open logfile

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 li

Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]

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 Sc

Re: [gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support

cess. 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 befor

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

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 si

[gmx-users] topolbuild 1.3, revision to topolbuild that incorporates OPLS-AA support

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

[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

Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field

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/lis

Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field

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

Re: [gmx-users] topolbuild

es 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 sear

Re: [gmx-users] amber force field in gromacs

n 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. Indianapol

Re: [gmx-users] Problem with topolbuild

oes 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. 40

Re: [gmx-users] Problem with topolbuild

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 fiel

Re: [gmx-users] Fatal Equilibration Errors

sion 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 li

Re: [gmx-users] Fatal Equilibration Errors

csf.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: > > ethaned

Re: [gmx-users] Energy Minimisation and Equilibration Problems

tion 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

Re: [gmx-users] Energy Minimisation and Equilibration Problems

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 Fm

Re: [gmx-users] Energy Minimisation and Equilibration Problems

s, 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 wha

Re: [gmx-users] Energy Minimisation and Equilibration Problems

erged 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 ? --

Re: [gmx-users] Energy Minimisation Values

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 t

[gmx-users] Re: MD Simulation Errors for Ethylene Glycol-Water System

nimization 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

Re: [gmx-users] Carbohydrate MD Simulation

s 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

Re: [gmx-users] problem with installation of topolbuild1.2.1

ems 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: Binar

Re: [gmx-users] Installing topolbuild

02022 ar 412041 1 42 2122 ar 4321421 @ -- Bruce D. Ray, Ph.D. Associate Scientist, and Operations Director NMR Center IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___

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

Re: [gmx-users] Installing topolbuild

e 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

Re: [gmx-users] Installing topolbuild

te, 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 Phys

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

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 f

[gmx-users] topolbuild 1.2.1, gromacs topology builder for gromacs and amber force field topologies

, 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

[gmx-users] topolbuild 1.2, gromacs topology builder extended to include gromacs united atoms force fields

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

[gmx-users] topolbuild 1.1.2, further revisions to an all-atoms model gromacs topology generator

. 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

[gmx-users] topolbuild 1.1.1, minor revisions to an all-atoms model gromacs topology generator

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