hello everyone ok justin iam sending you the link of images http://s48.photobucket.com/user/mittukhattri/media/Screenshot-3_zps81b0c070.png.html http://i48.photobucket.com/albums/f213/mittukhattri/Screenshot-3_zps81b0c070.png ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif
; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "backbone_posre.itp" #endif ; Include ligand topology #include "drag.itp" ; Ligand position restraints #ifdef DPOSRES_LIG #include "posre_UNK.itp" #endif ; Include POPC chain topology #include "popc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000000 1000000 1000000 2 2 1000000 1000000 1000000 3 3 1000000 1000000 1000000 #endif ; Include topology for ions #include "gromos53a6.ff/ions.itp" [ system ] ; Name Displayed atoms in water [ molecules ] ; Compound #mols Protein_chain_A 1 UNK 1 POPC 122 this is my topology i will add water and ions after the shrinking step i did't get inflategro2.pl script i used infltegro.pl kindly help On Tue, Jul 22, 2014 at 4:46 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/21/14, 11:30 AM, RINU KHATTRI wrote: > >> hello everyone >> >> thanks justin it works but problem is at the same place even one more >> problem ligand is out side the protein and protein is out side the popc >> > > So you've placed the ligand incorrectly or otherwise manipulated the > coordinates wrong. Given the absence of any other information, it's > impossible to suggest anything. > > -Justin > > > kindly help >> >> >> On Sat, Jul 19, 2014 at 7:39 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 7/19/14, 9:56 AM, RINU KHATTRI wrote: >>> >>> hello everyone >>>> >>>> i know justin -D is for minim.mdp not for topology i used simply D >>>> >>>> >>> That's still wrong. There should be no "D" or "-D" in the #ifdef >>> statement; it's cpp macro syntax. Please look at the block I provided >>> before: >>> >>> >>> #ifdef STRONG_POSRES >>> #include "strong_posre.itp" >>> #endif >>> >>> Use it exactly. Copy and paste it. Invoke it with "define = >>> -DSTRONG_POSRES" >>> >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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.