Re: [gmx-users] Re: Topology file
On 8/15/12 9:12 AM, Ankita naithani wrote: Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? Yes, #include statements for position restraint files are contained in each chain topology. -Justin On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani wrote: Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my protein. For instance, my topology file looks like this: ; Include forcefield parameters #include "gromos53a6.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_D.itp" #include "topol_Protein_chain_E.itp" #include "topol_Protein_chain_F.itp" #include "topol_Protein_chain_G.itp" ;Include ligand topology #include "FDP_Dp.itp" ; Include water topology #include "gromos53a6.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "gromos53a6.ff/ions.itp" But, after running pdb2gmx, I do get 4 posre files for all the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: Topology file
Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani wrote: > Hi, > > I noticed that in my topology file, there is no inclusion of position > restraint file for my protein. For instance, my topology file looks > like this: > > ; Include forcefield parameters > #include "gromos53a6.ff/forcefield.itp" > > ; Include chain topologies > #include "topol_Protein_chain_D.itp" > #include "topol_Protein_chain_E.itp" > #include "topol_Protein_chain_F.itp" > #include "topol_Protein_chain_G.itp" > > ;Include ligand topology > #include "FDP_Dp.itp" > > ; Include water topology > #include "gromos53a6.ff/spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > ; Include topology for ions > #include "gromos53a6.ff/ions.itp" > > > But, after running pdb2gmx, I do get 4 posre files for all the > individual chains. Do I need to add in them manually? Also, I am > unable to understand as to why did it not get included in the first > instance itself? I am using gromos53a6 force field. > > > Best Wishes, > > -- > Ankita Naithani -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: topology file
On 2011-12-24 13:08, Su Nh wrote: Dear Prof. van der Spoe Thank you for your responce. But I want to know if the charges in the topology files, which are built by ATB, are accurate and there is no need to re-calculate them or not? On the oder hand, what is the compatible parameters (basis set and method) with GROMOS force field? Thank you very much indeed su Ask the guys who made the website please. You can also check out http://virtualchemistry.org for OPLS & GAFF. Please put further questions on the mailing list. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: topology file generation for a modeled structure
On 08/02/10 19:40, bharat gupta wrote: Thanks for the help mdrun step is going on now .. but I wanna ask one thing that how can I visualize the minimized structure .. Search the GROMACS webpage for visualisation software suggestions. The structure which I used initially is the minimized structure or not ?? That's up to you - you wrote (and kept a record of) the grompp command line, remember? Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: topology file generation for a modeled structure
Thanks for the help mdrun step is going on now .. but I wanna ask one thing that how can I visualize the minimized structure .. The structure which I used initially is the minimized structure or not ?? Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: topology file generation for a modeled structure
Hello! Since you have modelled the structure, so the important thing is the position of the heavy atoms and not of the hydrogens, you can just do what GROMACS asks you to do: pdb2gmx . (all the things that you have to put) .. -ignh This flag will make pdb2gmx ignore the hydrogens and replace them. Hope it helps! Cheers, Annalisa --- Annalisa Bordogna - PhD. student Universita` degli Studi di Milano - Bicocca - Italy 2010/2/8, bharat gupta : > > Hi all, > > I have modelled a structure and I want to minimize it using GROMACS > but while generating the topology file using pdb2gmx command I am > getting the following error :- > > Atom HN1 in residue LEU 1 not found in rtp entry with 9 atoms > while sorting atoms. Maybe different protonation state. > Remove this hydrogen or choose a different protonation state. > Option -ignh will ignore all hydrogens in the input. > > > > > Can anyone help me out to rectify this error > > -- > Bharat > M.Sc. Bioinformatics (Final year) > Centre for Bioinformatics > Pondicherry University > Puducherry > India > Mob. +919962670525 > > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
[gmx-users] Re: topology file generation for a modeled structure
Hi all, I have modelled a structure and I want to minimize it using GROMACS but while generating the topology file using pdb2gmx command I am getting the following error :- Atom HN1 in residue LEU 1 not found in rtp entry with 9 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. Can anyone help me out to rectify this error -- Bharat M.Sc. Bioinformatics (Final year) Centre for Bioinformatics Pondicherry University Puducherry India Mob. +919962670525 -- gmx-users mailing listgmx-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
