kindly tell me sir how i can i add residue On Thu, Jun 15, 2017 at 2:04 AM, Rana Rehan Khalid <rrkha...@umich.edu> wrote:
> thanks justin > actually i want to know that how these values of column (atom name, type, > charge and charge group) we obtain for oxygen bonded with heme fe. is there > any program through which i find the parameter file for oxygen with heme > and nitric oxide with heme iron. if i just add the atom name type and > charge in the bonded type heme fe atoms is it work for me can you tell me > about any tutorial in which adding residue shows with examples that will be > very understandable. thanks > > On Wed, Jun 14, 2017 at 4:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 6/14/17 12:25 AM, Rana Rehan Khalid wrote: >> >>> Hi >>> I have read the chapter 5 of manual but i am confuse how can i add >>> residue >>> into heme atom of .rtp ff >>> this is the coordinate due to which error come >>> >>> HETATM 1529 O01 HEM 187 3.996 19.101 70.594 0.00 >>> 0.00 O >>> >>> kindly guide me how i can make changes in the rtp file and .atp so that >>> this error remove >>> here is the heme rtp part of my selected ff where i can add O01 and also >>> tell me these 4 column and these values and tell me which value i add for >>> O01 like (FE FE 0.40000 0 ) >>> >> >> You should refer back to the manual if the contents of these files are >> not clear. You're seeking to introduce new parameters for an oxygen-bound >> form of heme; this may require very complex parametrization work. >> Modifying an .rtp file is trivial; it's just text. Putting realistic >> parameters into it is a whole other matter. Check the literature for any >> existing efforts to avoid duplicated work. >> >> -Justin >> >> [ HEME ] >>> [ atoms ] >>> FE FE 0.40000 0 >>> NA NR -0.10000 0 >>> NB NR -0.10000 0 >>> NC NR -0.10000 0 >>> ND NR -0.10000 0 >>> CHA C -0.10000 1 >>> HHA HC 0.10000 1 >>> C1A C 0.00000 2 >>> C2A C 0.00000 2 >>> C3A C 0.00000 2 >>> C4A C 0.00000 2 >>> CMA CH3 0.00000 3 >>> CAA CH2 0.00000 4 >>> CBA CH2 0.00000 4 >>> CGA C 0.27000 5 >>> O1A OM -0.63500 5 >>> O2A OM -0.63500 5 >>> CHB C -0.10000 6 >>> HHB HC 0.10000 6 >>> C1B C 0.00000 7 >>> C2B C 0.00000 7 >>> C3B C 0.00000 7 >>> C4B C 0.00000 7 >>> CMB CH3 0.00000 8 >>> CAB CR1 0.00000 9 >>> CBB CH2 0.00000 9 >>> CHC C -0.10000 10 >>> HHC HC 0.10000 10 >>> C1C C 0.00000 11 >>> C2C C 0.00000 11 >>> C3C C 0.00000 11 >>> C4C C 0.00000 11 >>> CMC CH3 0.00000 12 >>> CAC CR1 0.00000 13 >>> CBC CH2 0.00000 13 >>> CHD C -0.10000 14 >>> HHD HC 0.10000 14 >>> C1D C 0.00000 15 >>> C2D C 0.00000 15 >>> C3D C 0.00000 15 >>> C4D C 0.00000 15 >>> CMD CH3 0.00000 16 >>> CAD CH2 0.00000 17 >>> CBD CH2 0.00000 17 >>> CGD C 0.27000 18 >>> O1D OM -0.63500 18 >>> O2D OM -0.63500 18 >>> >>> thanks >>> >>> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.