You have been provided there with the reference in which the parameters for the molecule were derived.
Read it! And determine yourself if it is applicable or not to what you are doing and the forcefield you are using. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Thursday, 9 June 2011 11:29 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Umbrella sampling of phosphate ion binding I found it in the /shared/top/ gmx.ff folder . Here's the file ; ; Force field based on GROMOS with new charges as described in ; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen: ; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic ; mottle virus coat protein in solution with phosphate ions ; Biophys. J. 71 pp. 2920-2932 (1996) ; [ moleculetype ] ; name nrexcl h2po4 4 [ atoms ] ; nr type resnr residu atom cgnr charge mass ; use charges from Janez Mavri 1 OA 1 PI O1 1 -0.777 2 OA 1 PI O2 1 -0.777 3 OM 1 PI O3 1 -0.943 4 OM 1 PI O4 1 -0.943 5 P 1 PI P 1 1.596 6 HO 1 PI H1 1 0.422 7 HO 1 PI H2 1 0.422 [ bonds ] ; ai aj funct c0 c1 5 1 1 1.637000e-01 5 2 1 1.637000e-01 5 3 1 1.478000e-01 5 4 1 1.478000e-01 6 1 1 0.943000e-01 7 2 1 0.943000e-01 [ angles ] ; ai aj ak funct c0 c1 2 5 1 1 1.015000e+02 400 3 5 1 1 1.059000e+02 4 5 1 1 1.082000e+02 3 5 2 1 1.059000e+02 4 5 2 1 1.082000e+02 4 5 3 1 1.248000e+02 6 1 5 1 1.082000e+02 7 2 5 1 1.082000e+02 [ dihedrals ] ; ai aj ak al funct 6 1 5 2 1 7 2 5 1 1 Can I use it or not ?? On Thu, Jun 9, 2011 at 10:26 AM, Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: bharat gupta wrote: does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug Probably not; check the .rtp file for your desired force field. server and after checking the topology I found that it has deleted of the hydrogen. See the PRODRG FAQ; this gets asked all the time. http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html No matter what PRODRG gives you, the charges will probably be useless anyway: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips So you're in for the difficult process of parameterization if no one's already developed parameters for your molecule: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu<mailto:jalem...@vt.edu>>> wrote: bharat gupta wrote: Hi Justin, I am having following doubts regarding umbrella sampling of phosphate ion binding to my protein . 1. As per the tutorial, I need to fix an immobile reference. In my case which region do I have to fix as my protein consists of one single chain. Since I am studying the binding and unbinding of ion, shall I fix the ion fixed. If it's so, then do I have to give a different chain name for it as my complex doesnot chain name for ion/ligand. You don't need an immobile reference just because my tutorial did. I had a particular need to do so. For your purpose, I highly doubt it's necessary. You're looking at small molecule-protein interactions, not protein-protein interactions. 2. What should be the size of box and how do I know where to place the protein's COM in box (the precise location). The absolute COM is somewhat irrelevant; all distances during pulling are relative. You can place the protein in a certain location in the box for convenience if you like. The box size must be greater than twice the pull distance, as explained in the tutorial. The amount that you wish to pull will dictate both the location of the protein and the box size. -Justin -- ==============================__========== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu<http://vt.edu> <http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> ==============================__========== -- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org<mailto: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<mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>>. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists> -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com<mailto:monu46...@yahoo.com> <mailto:monu46...@yahoo.com<mailto:monu46...@yahoo.com>> -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org<mailto: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<mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com<mailto:monu46...@yahoo.com>
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