Thank you I have generated the itp file from ATB. It works fine.
On Wed, Dec 21, 2016 at 7:48 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/19/16 1:23 PM, tasneem kausar wrote: > >> Thank you for reply >> What type of refinements are needed in topolgy file. >> I have created the topology file from pdb file. Mol2 was converted into >> pdb >> and sdf of pubchem was converted into mol2. >> So sdf to mol2 to pdb. >> And please suggest me the right choice of server for itp file generation. >> >> > Check the bond length parameters and make sure your coordinate file > matches the order of the atoms in the topology. Don't ignore warnings from > grompp. > > -Justin > > > Thanks in advance >> >> On 19 Dec 2016 18:31, "Justin Lemkul" <jalem...@vt.edu> wrote: >> >>> >>> >>> >>> On 12/19/16 5:31 AM, tasneem kausar wrote: >>> >>>> >>>> Thanks for reply >>>> >>>> I have visualized solvate.gro and em.gro. Some bonds that are not >>>> present >>>> in box.gro is seen in em.gro. >>>> I am giving you the link of the file to visualize. >>>> https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE >>>> https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM >>>> >>> >>> >>> You have an amide group that distorts, bringing the carbonyl C closer to >>> >> the amide proton, which VMD then fictitiously assigns as a C-H bond. The >> C-N bond is much too short. This suggests your topology is of >> insufficient >> quality for doing simulations and requires refinement. There is, of >> course, no actual bond there, as Mark has pointed out. Visualization >> software tries to guess where bonds should be based on interatomic >> distances. The topology is definitive. What you see on your screen is >> not. >> >>> >>> >>> I addition to that I have done energy minimization multiple times with >>>> steepest decent and conjugate gradient method. Potential energy value is >>>> negative in every minimization. When I am trying position restrain core >>>> dump with multiple lincs warning occurs. >>>> >>> >>> >>> Your topology needs work. It will not be stable for any simulation. >>> >>> -Justin >>> >>> >>> Please tell me how this problem would be resolved >>>> >>>> On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abra...@gmail.com >>>> > >>>> wrote: >>>> >>>> Hi, >>>>> >>>>> Your energy minimization literally cannot create bonds because those >>>>> are >>>>> already defined by your topology. See >>>>> >>>>> http://www.gromacs.org/Downloads/Related_Software/Visualizat >> ion_Software# >> >>> Topology_bonds_vs_Rendered_bonds >>>>> for what's probably going on. >>>>> >>>>> Mark >>>>> >>>>> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausa...@gmail.com> >>>>> wrote: >>>>> >>>>> Dear All >>>>>> >>>>>> >>>>>> I am using Acpype server to generate topology file of drug molecule to >>>>>> perform protein drug MD simulation. Acpype have generated the itp file >>>>>> >>>>> >>>>> and >>>>> >>>>>> >>>>>> other necessary for MD simulations. I am doing MD on gromacs 5.1.4 >>>>>> >>>>> >>>>> software >>>>> >>>>>> >>>>>> using amber99sb force field. When I have done energy minimization some >>>>>> unwanted bonds are formed in drug molecule. So the position restraint >>>>>> >>>>> is >> >>> not able to execute. The problem is due to the unusual bond in drug >>>>>> >>>>> atom. >> >>> When I used the itp file of PRODRG server position restraint goes >>>>>> successfully. I have used the gromos54a7 ff. But there is problem with >>>>>> >>>>> >>>>> the >>>>> >>>>>> >>>>>> charge present on the atom that comes from PRODRG. >>>>>> >>>>>> Please tell me how charge on the atom can be corrected in itp file of >>>>>> PRODRG. How the problem in energy minimization with the Acpype itp >>>>>> >>>>> will >> >>> >>>>> be >>>>> >>>>>> >>>>>> resolved. >>>>>> >>>>>> Thanks in Advance >>>>>> With Regards >>>>>> Tasneem >>>>>> -- >>>>>> 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. >>>>> >>>>> >>> -- >>> ================================================== >>> >>> 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. >> >> > -- > ================================================== > > 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.