Hi Tom !!! Can you guide to incorporate the AMBER parameter for ATP ( http://www.pharmacy.manchester.ac.uk/bryce/amber#cof) in ffamber. I am using ffamber for the simulation of Protein + ATP.
Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Jan 21, 2010 at 7:06 PM, Thomas Piggot <t.pig...@bristol.ac.uk>wrote: > If using an amber forcefield and GTP/GDP you can use the parameters on the > following website. I have used the ATP/ADP ones and have had no problems > with many different systems and ATP/ADP conformations with which I used to > test these parameters. > > http://www.pharmacy.manchester.ac.uk/bryce/amber#cof > > Tom > > > Justin A. Lemkul wrote: > >> >> >> Carla Jamous wrote: >> >>> Thank you Justin, >>> but I ran a simulation before this one with GTP & it worked fine. GDP & >>> GTP parameters are identical except for GDP having less atoms. >>> This is why I can't understand why I don't get an integer charge while I >>> did in my previous simulation. >>> >>> >> OK, but this still doesn't help anyone give you any advice. Please refer >> to my previous post - which case applies to you: almost integer, or way off? >> >> It is also potentially faulty logic to suggest that GDP parameters can be >> generated from GTP parameters by simply chopping off a phosphate. Under >> most force field parameter sets, the charges on the beta-phosphate will have >> to change since the electronic properties of the molecule are now different. >> >> -Justin >> >> Carla >>> >>> On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >>> jalem...@vt.edu>> wrote: >>> >>> >>> >>> Carla Jamous wrote: >>> >>> Hi, >>> >>> In order to run my simulation, I had to insert GDP parameters in >>> ffamber94 (the force field I'm using). >>> However, I'm having a problem with GDP charge. >>> the charge of every charge group in top file should be an >>> integer. But I'm getting a decimal charge which gives me >>> naturally a decimal total charge of my molecule. >>> I checked number of atoms, it's correct, their charge also. >>> But it seems it's having trouble adding charges & giving an >>> integer charge. >>> Does anyone have an idea where is the source of the problem? >>> >>> >>> What is the charge? If it is a small difference between an integer >>> and your charge (i.e., the difference between +1.9999 and +2) then >>> there is no problem. The issue there is the inherent limitation of >>> doing a lot of floating-point operations to sum the total charge. >>> If, however, you have a charge of +1.9256 when you wanted +2, then >>> your parameters are simply wrong. >>> >>> -Justin >>> >>> Thanks >>> >>> Carla >>> >>> >>> -- ======================================== >>> >>> 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/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/mailing_lists/users.php >>> >>> >>> >> > -- > Thomas Piggot > University of Bristol, UK. > > -- > 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/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 >
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