Dear Justin I want exactly this, that the distance between Au-S be stable around equilibrium value, For this purpose,Should I put the harmonic parameters related to the gold and sulfur in ffbonded file? Or I should consider AU-S connection as VonderWaals and put its epsilon and sidma in ffnonbonded file?
thank you Fatemeh Ramezani ________________________________ From: "gmx-users-requ...@gromacs.org" <gmx-users-requ...@gromacs.org> To: gmx-users@gromacs.org Sent: Tuesday, 18 December 2012, 14:30 Subject: gmx-users Digest, Vol 104, Issue 83 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than "Re: Contents of gmx-users digest..." Today's Topics: 1. merge .gro, .top files (Kieu Thu Nguyen) 2. Re: GPU running problem with GMX-4.6 beta2 (Albert) 3. Re: merge .gro, .top files (Tsjerk Wassenaar) 4. Re: merge .gro, .top files (Erik Marklund) 5. Re: merge .gro, .top files (Vedat Durmaz) 6. Re: Re: gold-S simulation (francesco oteri) ---------------------------------------------------------------------- Message: 1 Date: Tue, 18 Dec 2012 12:18:38 +0700 From: Kieu Thu Nguyen <kieuthu2...@gmail.com> Subject: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <CACrJSRgRHUbjqW+Zpfq=yfmcuh9ow68d2kmvklghez3acas...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT ------------------------------ Message: 2 Date: Tue, 18 Dec 2012 09:20:05 +0100 From: Albert <mailmd2...@gmail.com> Subject: Re: [gmx-users] GPU running problem with GMX-4.6 beta2 To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <50d02735.9030...@gmail.com> Content-Type: text/plain; charset=UTF-8; format=flowed On 12/17/2012 08:06 PM, Justin Lemkul wrote: > It seems to me that the system is simply crashing like any other that > becomes unstable. Does the simulation run at all on plain CPU? > > -Justin Thank you very much Justin, it's really helpful. I've checked that the structure after minization and found that there is some problem with my ligand. I regenerated the ligand toplogy with acpype, and resubmit for mimization and NVT. Now it goes well. So probably the problems comes from the incorrect ligand topolgy which make the system very unstable. best Albert ------------------------------ Message: 3 Date: Tue, 18 Dec 2012 09:30:04 +0100 From: Tsjerk Wassenaar <tsje...@gmail.com> Subject: Re: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <cabze1siujhgv4o8ndjfsnu4pxtketqmhxdi2i77vhp60nnj...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print "Merged gro file\n%5d" % (sum([len(i) for i in f]) - 3*len(f)) print "".join(["".join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com>wrote: > Dear All, > > I don't know which tools used to merge 2 files .gro, 2 files .top ? > Can i use trjcat ? > > Thanks ! > KT > -- > gmx-users mailing list gmx-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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada ------------------------------ Message: 4 Date: Tue, 18 Dec 2012 09:38:41 +0100 From: Erik Marklund <er...@xray.bmc.uu.se> Subject: Re: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <bd5228d7-229f-4e9c-9f03-66836dd50...@xray.bmc.uu.se> Content-Type: text/plain; charset=us-ascii 18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: > Hi KT, > > If you mean concatenating frames in .gro files, you can use trjcat or just > cat. If you mean merging the coordinates, it's a wee bit more complicated. > Since you also ask for top files, I guess that's the case. Here's a snippet > of python code that will do the trick: > > #!/usr/bin/env python > > import sys > > f = [open(i).readlines() for i in sys.argv[1:]] > print "Merged gro file\n%5d" % (sum([len(i) for i in f]) - 3*len(f)) > print "".join(["".join(i[2:-1]) for i in f]), > print f[0][-1] > > > For the top files, it is necessary to ensure all the moleculetypes are > #included, and that the [ molecules ] listing under [ system ] has the > right number and order of the molecules in the merged gro file. There's no > tool for that that I know of. In principle you could use grompp for checking that. It would print out a heap of warinngs/notes/errors if structure file and topology don't match. Erik > > Cheers, > > Tsjerk > > > On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com>wrote: > >> Dear All, >> >> I don't know which tools used to merge 2 files .gro, 2 files .top ? >> Can i use trjcat ? >> >> Thanks ! >> KT >> -- >> gmx-users mailing list gmx-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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > gmx-users mailing list gmx-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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html ------------------------------ Message: 5 Date: Tue, 18 Dec 2012 10:12:41 +0100 From: Vedat Durmaz <dur...@zib.de> Subject: Re: [gmx-users] merge .gro, .top files To: gmx-users@gromacs.org Message-ID: <50d03389.4030...@zib.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed there's also an executable topology merger available written in python called "gromacs_topology_merger.py" as part of a the software package "ZIBMolPy" designed for conformational analysis at https://github.com/CMD-at-ZIB/ZIBMolPy given (in the same directory) a topology file "topol.top" (argument 1) and two (or more) itp files "mol1.itp" and "mol2.itp" included in the top file, the tool writes out a new topology file (argument 2) merging the first two molecules from the include sequence of which itp files are given. note: the number of molecules to be merged should be 1 in the [ molecules ] section. if one of them is meant to appear multiple times in the merged topology, the process needs to be repeated accordingly. vedat Am 18.12.2012 09:38, schrieb Erik Marklund: > 18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar: > >> Hi KT, >> >> If you mean concatenating frames in .gro files, you can use trjcat or just >> cat. If you mean merging the coordinates, it's a wee bit more complicated. >> Since you also ask for top files, I guess that's the case. Here's a snippet >> of python code that will do the trick: >> >> #!/usr/bin/env python >> >> import sys >> >> f = [open(i).readlines() for i in sys.argv[1:]] >> print "Merged gro file\n%5d" % (sum([len(i) for i in f]) - 3*len(f)) >> print "".join(["".join(i[2:-1]) for i in f]), >> print f[0][-1] >> >> >> For the top files, it is necessary to ensure all the moleculetypes are >> #included, and that the [ molecules ] listing under [ system ] has the >> right number and order of the molecules in the merged gro file. There's no >> tool for that that I know of. > In principle you could use grompp for checking that. It would print out a > heap of warinngs/notes/errors if structure file and topology don't match. > > Erik > >> Cheers, >> >> Tsjerk >> >> >> On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen >> <kieuthu2...@gmail.com>wrote: >> >>> Dear All, >>> >>> I don't know which tools used to merge 2 files .gro, 2 files .top ? >>> Can i use trjcat ? >>> >>> Thanks ! >>> KT >>> -- >>> gmx-users mailing list gmx-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 >>> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Biocomputing Group >> Department of Biological Sciences >> 2500 University Drive NW >> Calgary, AB T2N 1N4 >> Canada >> -- >> gmx-users mailing list gmx-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 > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > ------------------------------ Message: 6 Date: Tue, 18 Dec 2012 10:52:17 +0100 From: francesco oteri <francesco.ot...@gmail.com> Subject: Re: [gmx-users] Re: gold-S simulation To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <cafqcp-nrppk_gfunffownyrdvf4k6jp4f3ngacrfuobx_r6...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear fatemeh, in the topology file there is a section called [ bonds ] where the covalent bonds are listed. You should add you bonds there. But I think modifing specbonds.dat is easier because it allows pdb2gmx to do the "dirty" job :) Anyway, f you have to simulate bond breaking, you can use Morse potential whose parameters can directly derived by the armonic form. Morse potential doesn't allow the bond breaking but the overall effect is very close! I have to admit I never used but only read about Morse potential so I cannot do practic advices! Francesco 2012/12/17 Justin Lemkul <jalem...@vt.edu> > > > On 12/17/12 4:01 PM, fatemeh ramezani wrote: > >> >> >> Dear Justin >> >> According to papers, I expect gold atom interacts with the sulfur atom of >> amino acid cysteine covalently. But in last email you said in the case of >> protein-Au This will not be true to add these parameters >> in topology file. Then in which file should I add the parameters >> between gold and sulfur? >> >> What do you suggest? How do I define for the program that can be >> established between these two atoms covalent bond ? >> >> > Bonds do not break and form in standard MD. For that, you need QM or > QM/MM type calculations. > > If there should be a bond between Cys and Au, you need to write that into > the topology or use the specbond.dat mechanism. pdb2gmx will not create > bonds between Au and Cys otherwise. The other modifications you have made, > as far as I can tell, are fine. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Cordiali saluti, Dr.Oteri Francesco ------------------------------ -- gmx-users mailing list gmx-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! End of gmx-users Digest, Vol 104, Issue 83 ****************************************** -- gmx-users mailing list gmx-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