How to edit the .hdb file On Thu, Mar 2, 2017 at 6:52 PM, RAHUL SURESH <drrahulsur...@gmail.com> wrote:
> I can manually parametrize my topology but to parametrize Hydrogen atoms > goes too tedious. > There must be any easy way.? > > On Thu, Mar 2, 2017 at 6:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 3/2/17 2:51 AM, Subashini .K wrote: >> >>> Did you try PRODRG server? >>> >>> >> Broken record time: the quality of PRODRG topologies is very low. One >> should always manually reparametrize the molecule, or use better servers >> like ATB. PRODRG and ATB produce GROMOS topologies, which are not useful if >> the goal is an OPLS-AA topology. >> >> -Justin >> >> >> >>> >>> ________________________________ >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL >>> SURESH <drrahulsur...@gmail.com> >>> Sent: Thursday, March 2, 2017 9:53 AM >>> To: gmx-us...@gromacs.org >>> Subject: Re: [gmx-users] topology >>> >>> Dear Justin >>> >>> Is there anything I can do to make this job easier? >>> >>> On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 3/1/17 2:19 PM, RAHUL SURESH wrote: >>>> >>>> Dear Justin >>>>> >>>>> What is the error here? >>>>> I don't understand it. >>>>> Can you be little more precise? >>>>> >>>>> >>>>> The long and short of it TopolGen is very crudely coded and atom order >>>> matters because the script makes a lot of assumptions. Your input PDB >>>> file >>>> has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure >>>> out what any of the actual functional groups are, so you get basically >>>> default atom types for everything. >>>> >>>> -Justin >>>> >>>> >>>> On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>>> >>>>> >>>>> >>>>>> On 2/28/17 3:24 AM, RAHUL SURESH wrote: >>>>>> >>>>>> This is my itp file(only a part) >>>>>> >>>>>>> >>>>>>> I have highlighted two errors.. there are 19 such errors. >>>>>>> If I can know the reason for the error exactly it would be of a great >>>>>>> help >>>>>>> to me. >>>>>>> >>>>>>> >>>>>>> TopolGen relies on atom ordering to guess what the proper parameters >>>>>>> >>>>>> should be. It's pretty limited in what it can do. A coordinate file >>>>>> that >>>>>> simply groups atoms by element is going to produce a totally garbage >>>>>> topology, unfortunately. >>>>>> >>>>>> -Justin >>>>>> >>>>>> >>>>>> [ atoms ] >>>>>> >>>>>>> ; nr type resnr residue atom cgnr charge mass >>>>>>> typeB chargeB massB >>>>>>> 1 opls_154 1 UNK O 0 -0.580921 >>>>>>> 15.99940 >>>>>>> 2 opls_154 1 UNK O 0 -0.635654 >>>>>>> 15.99940 >>>>>>> 3 opls_516 1 UNK C 1 -0.112257 >>>>>>> 12.01100 >>>>>>> 4 opls_516 1 UNK C 2 -0.163224 >>>>>>> 12.01100 >>>>>>> 5 opls_516 1 UNK C 3 0.228741 >>>>>>> 12.01100 >>>>>>> 6 opls_516 1 UNK C 4 -0.304756 >>>>>>> 12.01100 >>>>>>> 7 opls_516 1 UNK C 5 -0.312217 >>>>>>> 12.01100 >>>>>>> 8 opls_145 1 UNK C 6 0.120569 >>>>>>> 12.01100 >>>>>>> 9 opls_145 1 UNK C 7 0.151897 >>>>>>> 12.01100 >>>>>>> 10 opls_145 1 UNK C 8 0.231044 >>>>>>> 12.01100 >>>>>>> 11 opls_516 1 UNK C 9 -0.401751 >>>>>>> 12.01100 >>>>>>> 12 opls_516 1 UNK C 10 -0.403094 >>>>>>> 12.01100 >>>>>>> 13 opls_145 1 UNK C 11 -0.150352 >>>>>>> 12.01100 >>>>>>> 14 opls_145 1 UNK C 12 0.193129 >>>>>>> 12.01100 >>>>>>> 15 opls_145 1 UNK C 13 -0.161115 >>>>>>> 12.01100 >>>>>>> 16 opls_516 1 UNK C 14 -0.471874 >>>>>>> 12.01100 >>>>>>> 17 opls_145 1 UNK C 15 0.100725 >>>>>>> 12.01100 >>>>>>> 18 opls_145 1 UNK C 16 -0.153943 >>>>>>> 12.01100 >>>>>>> 19 opls_516 1 UNK C 17 -0.330577 >>>>>>> 12.01100 >>>>>>> 20 opls_516 1 UNK C 18 -0.229875 >>>>>>> 12.01100 >>>>>>> 21 opls_135 1 UNK C 19 -0.229884 >>>>>>> 12.01100 >>>>>>> 22 opls_135 1 UNK C 20 -0.237230 >>>>>>> 12.01100 >>>>>>> 23 opls_135 1 UNK C 21 -0.404861 >>>>>>> 12.01100 >>>>>>> 24 opls_140 1 UNK H 21 0.135257 >>>>>>> 1.00800 >>>>>>> 25 opls_140 1 UNK H 21 0.154010 >>>>>>> 1.00800 >>>>>>> 26 opls_140 1 UNK 2H 21 0.142643 >>>>>>> 1.00800 >>>>>>> 27 opls_140 1 UNK 1H 21 0.133623 >>>>>>> 1.00800 >>>>>>> 28 opls_140 1 UNK 2H 21 0.137323 >>>>>>> 1.00800 >>>>>>> 29 opls_140 1 UNK 1H 21 0.167475 >>>>>>> 1.00800 >>>>>>> 30 opls_140 1 UNK 1H 21 0.135348 >>>>>>> 1.00800 >>>>>>> 31 opls_140 1 UNK 2H 21 0.153851 >>>>>>> 1.00800 >>>>>>> 32 opls_140 1 UNK 3H 21 0.138487 >>>>>>> 1.00800 >>>>>>> 33 opls_140 1 UNK 1H 21 0.137087 >>>>>>> 1.00800 >>>>>>> 34 opls_140 1 UNK 2H 21 0.146500 >>>>>>> 1.00800 >>>>>>> 35 opls_140 1 UNK 3H 21 0.148972 >>>>>>> 1.00800 >>>>>>> 36 opls_140 1 UNK H 21 0.103605 >>>>>>> 1.00800 >>>>>>> 37 opls_140 1 UNK H 21 0.127061 >>>>>>> 1.00800 >>>>>>> 38 opls_140 1 UNK 1H 21 0.143100 >>>>>>> 1.00800 >>>>>>> 39 opls_140 1 UNK 2H 21 0.137525 >>>>>>> 1.00800 >>>>>>> 40 opls_140 1 UNK 3H 21 0.140672 >>>>>>> 1.00800 >>>>>>> 41 opls_140 1 UNK H 21 0.106416 >>>>>>> 1.00800 >>>>>>> 42 opls_140 1 UNK 1H 21 0.134610 >>>>>>> 1.00800 >>>>>>> 43 opls_140 1 UNK 2H 21 0.126890 >>>>>>> 1.00800 >>>>>>> 44 opls_140 1 UNK 2H 21 0.132690 >>>>>>> 1.00800 >>>>>>> 45 opls_140 1 UNK 1H 21 0.124796 >>>>>>> 1.00800 >>>>>>> 46 opls_140 1 UNK H 21 0.371894 >>>>>>> 1.00800 >>>>>>> 47 opls_140 1 UNK 1H 21 0.120642 >>>>>>> 1.00800 >>>>>>> 48 opls_140 1 UNK 2H 21 0.117792 >>>>>>> 1.00800 >>>>>>> 49 opls_140 1 UNK 2H 21 0.125342 >>>>>>> 1.00800 >>>>>>> 50 opls_140 1 UNK 1H 21 0.122930 >>>>>>> 1.00800 >>>>>>> 51 opls_140 1 UNK 1H 21 0.130012 >>>>>>> 1.00800 >>>>>>> 52 opls_140 1 UNK 2H 21 0.129674 >>>>>>> 1.00800 >>>>>>> 53 opls_140 1 UNK 3H 21 0.131255 >>>>>>> 1.00800 >>>>>>> >>>>>>> [ bonds ] >>>>>>> ; ai aj funct >>>>>>> 1 5 1 ; O C >>>>>>> 1 10 1 ; O C >>>>>>> 2 14 1 ; O C >>>>>>> *2 46 1 ; O H* >>>>>>> >>>>>>> 3 4 1 ; C C >>>>>>> 3 5 1 ; C C >>>>>>> 3 6 1 ; C C >>>>>>> 3 24 1 ; C H >>>>>>> 4 7 1 ; C C >>>>>>> 4 8 1 ; C C >>>>>>> 4 25 1 ; C H >>>>>>> 5 11 1 ; C C >>>>>>> 5 12 1 ; C C >>>>>>> 6 13 1 ; C C >>>>>>> 6 26 1 ; C 2H >>>>>>> 6 27 1 ; C 1H >>>>>>> 7 9 1 ; C C >>>>>>> 7 28 1 ; C 2H >>>>>>> 7 29 1 ; C 1H >>>>>>> 8 10 1 ; C C >>>>>>> 8 14 1 ; C C >>>>>>> 9 13 1 ; C C >>>>>>> 9 16 1 ; C C >>>>>>> 10 15 1 ; C C >>>>>>> 11 30 1 ; C 1H >>>>>>> 11 31 1 ; C 2H >>>>>>> 11 32 1 ; C 3H >>>>>>> 12 33 1 ; C 1H >>>>>>> 12 34 1 ; C 2H >>>>>>> 12 35 1 ; C 3H >>>>>>> *13 36 1 ; C H* >>>>>>> >>>>>>> 14 18 1 ; C C >>>>>>> 15 17 1 ; C C >>>>>>> 15 37 1 ; C H >>>>>>> 16 38 1 ; C 1H >>>>>>> 16 39 1 ; C 2H >>>>>>> 16 40 1 ; C 3H >>>>>>> 17 18 1 ; C C >>>>>>> 17 19 1 ; C C >>>>>>> 18 41 1 ; C H >>>>>>> 19 20 1 ; C C >>>>>>> 19 42 1 ; C 1H >>>>>>> 19 43 1 ; C 2H >>>>>>> 20 21 1 ; C C >>>>>>> 20 44 1 ; C 2H >>>>>>> 20 45 1 ; C 1H >>>>>>> 21 22 1 ; C C >>>>>>> 21 47 1 ; C 1H >>>>>>> 21 48 1 ; C 2H >>>>>>> 22 23 1 ; C C >>>>>>> 22 49 1 ; C 2H >>>>>>> 22 50 1 ; C 1H >>>>>>> 23 51 1 ; C 1H >>>>>>> 23 52 1 ; C 2H >>>>>>> 23 53 1 ; C 3H >>>>>>> >>>>>>> On Tue, Feb 28, 2017 at 3:57 AM, Justin Lemkul <jalem...@vt.edu> >>>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 2/27/17 12:49 AM, RAHUL SURESH wrote: >>>>>>>> >>>>>>>> I am explaining my issues regarding complex simulation. >>>>>>>> >>>>>>>> >>>>>>>>> I have 200ns conformer(OPLS FF) >>>>>>>>> >>>>>>>>> I have generated my ligand gro and itp file.(Using topolgen1_1) >>>>>>>>> >>>>>>>>> I have edited my protein gro file and made it into complex file as >>>>>>>>> per >>>>>>>>> the >>>>>>>>> tutorials. >>>>>>>>> >>>>>>>>> I have made changes to my topol.top file. >>>>>>>>> >>>>>>>>> Now in my command for em.mdp I am getting 19 errors stating "NO >>>>>>>>> DEFAULT >>>>>>>>> BOND TYPE, ANGLE TYPE, ETC." >>>>>>>>> >>>>>>>>> Can you guide me with this? >>>>>>>>> >>>>>>>>> >>>>>>>>> This means the atom type assignment makes reference to bonded >>>>>>>>> parameters >>>>>>>>> >>>>>>>>> that don't exist. That means one of two things: (1) either the >>>>>>>> atom >>>>>>>> type >>>>>>>> assignment is incorrect, requiring manual correction (as the script >>>>>>>> warns >>>>>>>> you, as it makes a lot of assumptions and is therefore rather dumb >>>>>>>> sometimes) or (2) you simply have a molecule for which parameters do >>>>>>>> not >>>>>>>> exist, requiring manual parametrization. For OPLS-AA, this >>>>>>>> requires QM >>>>>>>> calculations to get things like equilibrium geometries, vibrational >>>>>>>> frequencies, and dihedral potential energy scans. >>>>>>>> >>>>>>>> >>>>>>>> -Justin >>>>>>>> >>>>>>>> -- >>>>>>>> ================================================== >>>>>>>> >>>>>>>> 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 >>>>>>>> >>>>>>> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]< >>> http://mackerell.umaryland.edu/~jalemkul> >>> >>> Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland >>> .edu/~jalemkul> >>> mackerell.umaryland.edu >>> Welcome to my site! To learn more about me and the work I am doing, >>> please use the navigation links above. >>> >>> >>> >>>>>>>> ================================================== >>>>>>>> -- >>>>>>>> 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. >>>> >>>> >>> >>> >>> -- >>> *Regards,* >>> *Rahul Suresh* >>> *Research Scholar* >>> *Bharathiar University* >>> *Coimbatore* >>> -- >>> 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. >> > > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.