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 ? many thanks Fatemeh Ramezani ________________________________ From: "gmx-users-requ...@gromacs.org" <gmx-users-requ...@gromacs.org> To: gmx-users@gromacs.org Sent: Monday, 17 December 2012, 1:47 Subject: gmx-users Digest, Vol 104, Issue 73 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. Re: Parametrisation of the cyclic nucleotides in Gromos force fields (James Starlight) 2. Re: Parametrisation of the cyclic nucleotides in Gromos force fields (Justin Lemkul) 3. Re: gold-S simulation (fatemeh ramezani) 4. Re: gold-S simulation (fatemeh ramezani) 5. Re: gold-S simulation (francesco oteri) 6. Box Pressure on individual box walls (John Doe) 7. Re: Box Pressure on individual box walls (David van der Spoel) 8. Re: gold-S simulation (Justin Lemkul) ---------------------------------------------------------------------- Message: 1 Date: Sun, 16 Dec 2012 19:34:57 +0400 From: James Starlight <jmsstarli...@gmail.com> Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <CAALQopzp6xCweeYWRcmMsZNYDnEvg_=gjpqofrlazphv5dd...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would be assigned as the backbone. That lines were added after grompp produce error about unknown cmap for that 5 atoms of the chromophore. Should the 24 24 \ be removed from each line of the chromophore cmap ? James ------------------------------ Message: 2 Date: Sun, 16 Dec 2012 11:12:35 -0500 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <50cdf2f3.4030...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 12/16/12 10:34 AM, James Starlight wrote: > Justin, thanks again for explanation. > So the first 5 atoms in cmap.it correspond to the starting sequence of > the backbone atoms of the amino acid doesnt it ? So what is the 24 24 > numbers at the end of each cmap line ? Probably something related to how Gromacs tools read in the CMAP data. I don't have time to go through the code to find exactly how it's used. > E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would > be assigned as the backbone. That lines were added after grompp > produce error about unknown cmap for that 5 atoms of the chromophore. > Should the 24 24 \ be removed from each line of the chromophore cmap ? > You shouldn't be modifying anything about cmap.itp, nor should those numbers be present in your .rtp file. Your [cmap] directive in the .rtp entry should contain a sequence of 5 atom names to which the CMAP corrections are applied. -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 ======================================== ------------------------------ Message: 3 Date: Sun, 16 Dec 2012 09:58:16 -0800 (PST) From: fatemeh ramezani <fr_...@yahoo.com> Subject: Re: [gmx-users] gold-S simulation To: "gmx-users-requ...@gromacs.org" <gmx-users-requ...@gromacs.org>, "gmx-users@gromacs.org" <gmx-users@gromacs.org>, "gmx-users-ow...@gromacs.org" <gmx-users-ow...@gromacs.org> Message-ID: <1355680696.17757.yahoomail...@web113504.mail.gq1.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Dear francesco I extract gold parameter from papers that I attached them for you. But for gold and other atom parameters, you should calculate them using common combination rule. Fatemeh Ramezani ________________________________ ------------------------------ Message: 4 Date: Sun, 16 Dec 2012 10:00:03 -0800 (PST) From: fatemeh ramezani <fr_...@yahoo.com> Subject: Re: [gmx-users] gold-S simulation To: "gmx-users-requ...@gromacs.org" <gmx-users-requ...@gromacs.org>, "gmx-users@gromacs.org" <gmx-users@gromacs.org>, "gmx-users-ow...@gromacs.org" <gmx-users-ow...@gromacs.org> Message-ID: <1355680803.57169.yahoomail...@web113507.mail.gq1.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani ________________________________ ------------------------------ Message: 5 Date: Sun, 16 Dec 2012 19:11:14 +0100 From: francesco oteri <francesco.ot...@gmail.com> Subject: Re: [gmx-users] gold-S simulation To: fatemeh ramezani <fr_...@yahoo.com>, Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: "gmx-users-ow...@gromacs.org" <gmx-users-ow...@gromacs.org>, "gmx-users-requ...@gromacs.org" <gmx-users-requ...@gromacs.org> Message-ID: <cafqcp-olnqncy2fudfeixeff9ao4dmgaonnufi1gasx1e4_...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and the Au atom to which it is supposed to be bound. If the distance is stable around the equilibrium value you can say that the interaction is still present Francesco 2012/12/16 fatemeh ramezani <fr_...@yahoo.com> > > > hi > thanks for your attention, > all itp files are in OPLSAA forcefield folder that I attached it for you. > > > > Fatemeh Ramezani > > > ________________________________ > > -- > 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 > -- Cordiali saluti, Dr.Oteri Francesco ------------------------------ Message: 6 Date: Sun, 16 Dec 2012 20:09:07 +0000 From: John Doe <helstr...@hotmail.com> Subject: [gmx-users] Box Pressure on individual box walls To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> Message-ID: <blu169-w126df4bba792e2b92d3e7a8b4...@phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hello All, I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis. Thank you for your time. ------------------------------ Message: 7 Date: Sun, 16 Dec 2012 21:45:47 +0100 From: David van der Spoel <sp...@xray.bmc.uu.se> Subject: Re: [gmx-users] Box Pressure on individual box walls To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <50ce32fb.9050...@xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2012-12-16 21:09, John Doe wrote: > > Hello All, > > I was wondering if it's possible to get the pressure on individual walls of a > pbc cubic box. I specifically want the pressure on the walls perpendicular > to the x, y, z axis. > g_energy will do it. > Thank you for your time. > -- > 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 > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------ Message: 8 Date: Sun, 16 Dec 2012 17:15:56 -0500 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] gold-S simulation To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <50ce481c.2020...@vt.edu> Content-Type: text/plain; charset=UTF-8; format=flowed On 12/16/12 1:11 PM, francesco oteri wrote: > Hi fatemeh, > thank you for the references. Regarding your problem, what does it means > you don't see any interaction? > Is it possible it is just a problem of the visualization software. To be > sure, you could monitor the distance > between any S atom and the Au atom to which it is supposed to be bound. If > the distance is stable around > the equilibrium value you can say that the interaction is still present > In addition, if one is expecting some sort of covalent association, it must be defined in the topology. This will not be true in the case of protein-Au interactions unless one makes appropriate entries in specbond.dat, similar to heme, or manual addition. Bonded parameters are useless unless there is a bond :) -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 ======================================== ------------------------------ -- 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 73 ****************************************** -- 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
