[gmx-users] Bad box in protein.gro
Hi all, I recently started molecular dynamics with gromacs performing protein-ligand simulations for my project first i worked out example from justin tutorials on protein ligand system and trying to apply to my protein and ligand. First i generated topology for my protein using pdbgmx and then i used PRODRG tool ligand topology has been generated then i included ligand.itp file in topol.top file and pasted ligand.gro which is generated from PRODRG tool in protein.gro as suggested in tutorial but problem comes now while running editconf as follows warning bad box editconf -f protein .gro -o box.gro -bt cubic -d 1.0 *WARNING: Bad box in file protein.gro* Generated a cubic box5.553 x4.382 x4.434 Read 2053 atoms Volume: 107.894 nm^3, corresponds to roughly 48500 electrons No velocities found system size : 5.553 4.382 4.434 (nm) diameter: 6.093 (nm) center : 0.068 -0.079 0.153 (nm) box vectors : 5.553 4.382 4.434 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 107.89 (nm^3) shift : 3.978 4.126 3.894 (nm) new center : 4.047 4.047 4.047 (nm) new box vectors : 8.093 8.093 8.093 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 530.06 (nm^3) Actually this problem is already been raised from some one else in gromacs discussion list i tried to use that solution but it is not helping me Can any body tell me where i am going wrong.. Thanks in advance Nitin -- 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
[gmx-users] How to fit ligand in specific site in protein in simulation
Hi all, I am working on protein - ligand molecular dynamics simulation using gromacs. I have a protein in which i know binding site which is composed of 5 residues and i have one ligand i have to place this in binding site. Can any body tell me how to do place this ligand to binding site Thanks in advance Cheers -- Sainitin D -- 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] How to fit ligand in specific site in protein in simulation
Hi gontchar, I have done docking analysis using autodock using that ligand and binding site but i want to do molecular dynamics (MD) using gromacs of same ligand and binding site of my protein. Thats why i want to know how to place ligand in specific binding site and run MD using gromacs. Thanks, Nitin On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар wrote: > I think you have to use some special programm for this purpose. > AutoDock, for example, will be the right choice. > > 2012/4/12 sai nitin : > > Hi all, > > > > I am working on protein - ligand molecular dynamics simulation using > > gromacs. I have a protein in which i know binding site which is composed > of > > 5 residues and i have one ligand i have to place this in binding site. > > > > Can any body tell me how to do place this ligand to binding site > > > > Thanks in advance > > > > > > Cheers > > -- > > > > Sainitin D > > > > > > -- > > 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 > > > > -- > > Андрей Гончар > -- > 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 > -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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] How to fit ligand in specific site in protein in simulation
hi rama david, Thank you for suggestion i looked up how to convert docked structure into PDB file it is described here http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock But i have one doudt about which structure to take should i consider docking results produced by autodock DLG file (docking log file) which consists of different docked conformations OR Should i consider complex PDB file (which consists of both protein + ligand) Thanks in advance, Sainitin On Thu, Apr 12, 2012 at 10:57 AM, rama david wrote: > Hi sai, > you have to used docked structure to simulation . > 1st convert the dock structure ,that you concider imptortant for > your further study to pdb file (As you used autodock for docking ). > Then perform MD on that structure. > > Have a nice day... > > > On Thu, Apr 12, 2012 at 2:14 PM, sai nitin wrote: > >> Hi gontchar, >> >> I have done docking analysis using autodock using that ligand and binding >> site but i want to do molecular dynamics (MD) using gromacs of same ligand >> and binding site of my protein. Thats why i want to know how to place >> ligand in specific binding site and run MD using gromacs. >> >> Thanks, >> Nitin >> >> >> On Thu, Apr 12, 2012 at 10:34 AM, Андрей Гончар wrote: >> >>> I think you have to use some special programm for this purpose. >>> AutoDock, for example, will be the right choice. >>> >>> 2012/4/12 sai nitin : >>> > Hi all, >>> > >>> > I am working on protein - ligand molecular dynamics simulation using >>> > gromacs. I have a protein in which i know binding site which is >>> composed of >>> > 5 residues and i have one ligand i have to place this in binding site. >>> > >>> > Can any body tell me how to do place this ligand to binding site >>> > >>> > Thanks in advance >>> > >>> > >>> > Cheers >>> > -- >>> > >>> > Sainitin D >>> > >>> > >>> > -- >>> > 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 >>> >>> >>> >>> -- >>> >>> Андрей Гончар >>> -- >>> 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 >>> >> >> >> >> -- >> >> Sainitin D >> PhD student >> Bioinformatics Group >> Biotechnology Center >> Technische Universität Dresden >> Tatzberg 47/49 >> 01307 Dresden, Germany >> Tel Lab:+49 (0)351 463 40060 >> >> -- >> 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 >> > > > -- > 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 > -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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
[gmx-users] Protein ligand molecular dynamics simulation
Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool ( http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? Thanks in advance -- Sainitin D -- 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] Protein ligand molecular dynamics simulation
Hi Justin, I generated topologies of my protein using PDB2GMX (charmm27 FF) and ligand topology using swissparam tool using Charmm force field i included ligand.itp file in topol.top of protein. And i used docked complex structure (protein + ligand) from docking analysis and generated boxed.pdb next i created solvated.pdb using (editconf and genbox tools) and also checked SOL molecules updated in topol.top file next i checked solvated.pdb file in pymol my ligand is in correct place in protein the way i wanted but problem came after this while using grompp I used grompp tool to minimize this solvated.pdb it is showing following error..using em.mdp Fatal Error number of coordinates in coordinate file (solvated.pdb, 51540) does not match topology (topol.top, 52756) I know this is commonly known issue for new users of gromacs. I looked up in gmx-archive list couldnt find optimal solution for my problem.. Let me know how to solve this ...issue... Cheers, Nitin On Mon, Apr 16, 2012 at 5:03 PM, Justin A. Lemkul wrote: > > > sai nitin wrote: > >> Hi all, >> >> I have done complex (protein + ligand) complex from autodock software >> using this complex im trying to follow >> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >> gmx-tutorials/complex/01_**pdb2gmx.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html> >> tutorial >> >> But when i take complex structure directly from autodock result and run >> PDB2GMX it will give error because it is not recognizing ligand topology >> which is in complex structure. >> Then i followed justin tutorial took protein alone and applied Charmm27 >> Force field and used generate ligand topologies using Swissparam tool ( >> http://swissparam.ch/) when i do Editconf and created cubic box ligand >> is going away from protein. >> >> Actually my main task to place ligand in paraticular binding site in my >> protein and perform molecular dynamics. >> >> Can any body tell me how to do this..? >> >> > Whatever you're doing is changing the coordinates that you originally had. > You don't want to do that. > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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
[gmx-users] PDB2GMX error in charmm27 Forcefield
Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 178. Can any body tell me how to solve this... Regards, -- Sainitin D -- 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
[gmx-users] crude interaction energy using g_energy
Dear all, Recently i performed two 15ns simulation of protein-ligand systems using gromacs of my interest...and using g_energy tool..i calculated crude interaction energy based on short-‐range energy components Eint = + . ...I got two Eints for two simulations 1) Eint = -51.003 Kcal/mol (first simulation) 2) Eint = -26.615 Kcal/mol (second simulation) Can anybody tell me what meaning can i make out of it...means is first simulation is more stable than second one..or vice versa... Thanks in advance Regards -- Sainitin D -- 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
[gmx-users] Linear Interaction energy calculations
Dear all, I recently started protein ligand simulation using gromacs my aim is to calculate binding free energies after simulations...I adapted justin tutorial and done 10 ns MD simulations using CHARMM FF and now going through LIE (Linear Interaction Energie method) g_lie in gromacs.. And came across that to perform LIE using gromacs involves two MD simulations one with protein - ligand simulation in solvent (which i finished)..and another with ligand only in solution in this step i got stuck can any body tell or suggest some tutorials to perform MD simulations for only ligand Thanks in advance -- Sainitin D -- 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] Error in ligand coordinate file
Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Charmm 27 FF second one is simulate ligand in water...which is the step i got stuck i know it is simple but couldnt get through first step it self preparing ligand coordinate file which i already have as follows i ran PDB2gmx to generate topol.top file but couldnt succeed.. ligand coordinate file is given below ATOM 1 N -13.006 -12.965 -0.251 1.00 0.00 N ATOM 2 C -13.386 -13.020 1.035 1.00 0.00 C ATOM 3 C1 -13.037 -14.131 1.869 1.00 0.00 C ATOM 4 C2 -12.284 -14.007 -0.761 1.00 0.00 C ATOM 5 N1 -11.897 -15.079 0.059 1.00 0.00 N ATOM 6 C3 -12.288 -15.172 1.391 1.00 0.00 C ATOM 7 N2 -13.547 -13.886 3.036 1.00 0.00 N ATOM 8 N3 -14.076 -12.193 1.759 1.00 0.00 N ATOM 9 C4 -14.163 -12.729 2.956 1.00 0.00 C ATOM 10 N4 -11.887 -13.919 -2.092 1.00 0.00 N ATOM 11 H -11.305 -15.802 -0.326 1.00 0.00 H ATOM 12 H1 -12.027 -12.978 -2.454 1.00 0.00 H ATOM 13 C5 -11.368 -14.845 -3.008 1.00 0.00 C ATOM 14 C6 -11.534 -14.731 -4.394 1.00 0.00 C ATOM 15 C7 -11.032 -15.710 -5.270 1.00 0.00 C ATOM 16 C8 -10.360 -16.822 -4.750 1.00 0.00 C ATOM 17 C9 -10.189 -16.950 -3.375 1.00 0.00 C ATOM 18 C10 -10.690 -15.970 -2.515 1.00 0.00 C ATOM 19 C11 -11.203 -15.559 -6.724 1.00 0.00 C ATOM 20 C12 -12.302 -15.958 -7.389 1.00 0.00 C ATOM 21 O -11.918 -16.240 2.152 1.00 0.00 O ATOM 22 H2 -11.168 -16.702 1.710 1.00 0.00 H ATOM 23 H3 -14.661 -12.289 3.746 1.00 0.00 H ATOM 24 H4 -12.034 -13.914 -4.779 1.00 0.00 H ATOM 25 H5 -9.992 -17.547 -5.386 1.00 0.00H ATOM 26 H6 -9.692 -17.769 -2.991 1.00 0.00H ATOM 27 H7 -10.559 -16.076 -1.497 1.00 0.00 H ATOM 28 H8 -10.438 -15.123 -7.263 1.00 0.00 H ATOM 29 H9 -13.084 -16.397 -6.878 1.00 0.00 H ATOM 30 H10 -12.364 -15.825 -8.411 1.00 0.00 H Running PDB2gmx gives error as follows Fatal error: Residue '-13.' not found in residue topology database Can any tell me what is wrong in my coordinate file Thanks. Nitin -- 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
Re: [gmx-users] Error in ligand coordinate file
Hi justin, Thanks for reply now i have ligand corrdinate file as follows ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C ATOM 3 C A -13.037 -14.131 1.869 -0.32 -0.03 C ATOM 4 C A -12.284 -14.007 -0.761 -0.21 0.02 C ATOM 5 N A -11.897 -15.079 0.059 -0.24 -0.01 N ATOM 6 C A -12.288 -15.172 1.391 -0.37 0.01 C ATOM 7 N A -13.547 -13.886 3.036 -0.34 0.14 N ATOM 8 N A -14.076 -12.193 1.759 -0.27 0.01 N ATOM 9 C A -14.163 -12.729 2.956 -0.29 -0.08 C ATOM 10 N A -11.887 -13.919 -2.092 -0.05 0.04 N ATOM 11 H A -11.305 -15.802 -0.326 -0.11 -0.03 H ATOM 12 H A -12.027 -12.978 -2.454 -0.07 -0.16 H ATOM 13 C A -11.368 -14.845 -3.008 -0.39 0.00 C ATOM 14 C A -11.534 -14.731 -4.394 -0.49 0.00 C ATOM 15 C A -11.032 -15.710 -5.270 -0.32 0.00 C ATOM 16 C A -10.360 -16.822 -4.750 -0.24 0.00 C ATOM 17 C A -10.189 -16.950 -3.375 -0.33 0.00 C ATOM 18 C A -10.690 -15.970 -2.515 -0.42 0.00 C ATOM 19 C A -11.203 -15.559 -6.724 -0.27 0.00 C ATOM 20 C A -12.302 -15.958 -7.389 -0.19 0.02 C ATOM 21 O A -11.918 -16.240 2.152 -0.14 -0.09 O ATOM 22 H A -11.168 -16.702 1.710 -0.26 -0.13 H END Still not working Fatal error: Atom N in residue A 0 was not found in rtp entry RA with 32 atoms while sorting atoms. Any help ?? Thanks, Nitin On Tue, Aug 7, 2012 at 11:42 AM, Justin Lemkul wrote: > > > On 8/7/12 5:08 AM, sai nitin wrote: >> >> Hi all, >> >> Recently i performed protein ligand complex simulation my aim is to >> compute free energy values using g_lie..i came across that to perform >> g_lie analysis one should two 2 MD simulation one is protein ligand >> complex simulation (this is done ) used Charmm 27 FF second one is >> simulate ligand in water...which is the step i got stuck i know it is >> simple but couldnt get through first step it self preparing ligand >> coordinate file which i already have as follows i ran PDB2gmx to >> generate topol.top file but couldnt succeed.. ligand coordinate file >> is given below >> >> ATOM 1 N -13.006 -12.965 -0.251 1.00 0.00 N >> ATOM 2 C -13.386 -13.020 1.035 1.00 0.00 C >> ATOM 3 C1 -13.037 -14.131 1.869 1.00 0.00 C >> ATOM 4 C2 -12.284 -14.007 -0.761 1.00 0.00 C >> ATOM 5 N1 -11.897 -15.079 0.059 1.00 0.00 N >> ATOM 6 C3 -12.288 -15.172 1.391 1.00 0.00 C >> ATOM 7 N2 -13.547 -13.886 3.036 1.00 0.00 N >> ATOM 8 N3 -14.076 -12.193 1.759 1.00 0.00 N >> ATOM 9 C4 -14.163 -12.729 2.956 1.00 0.00 C >> ATOM 10 N4 -11.887 -13.919 -2.092 1.00 0.00 N >> ATOM 11 H -11.305 -15.802 -0.326 1.00 0.00 H >> ATOM 12 H1 -12.027 -12.978 -2.454 1.00 0.00 H >> ATOM 13 C5 -11.368 -14.845 -3.008 1.00 0.00 C >> ATOM 14 C6 -11.534 -14.731 -4.394 1.00 0.00 C >> ATOM 15 C7 -11.032 -15.710 -5.270 1.00 0.00 C >> ATOM 16 C8 -10.360 -16.822 -4.750 1.00 0.00 C >> ATOM 17 C9 -10.189 -16.950 -3.375 1.00 0.00 C >> ATOM 18 C10 -10.690 -15.970 -2.515 1.00 0.00 C >> ATOM 19 C11 -11.203 -15.559 -6.724 1.00 0.00 C >> ATOM 20 C12 -12.302 -15.958 -7.389 1.00 0.00 C >> ATOM 21 O -11.918 -16.240 2.152 1.00 0.00 O >> ATOM 22 H2 -11.168 -16.702 1.710 1.00 0.00 H >> ATOM 23 H3 -14.661 -12.289 3.746 1.00 0.00 H >> ATOM 24 H4 -12.034 -13.914 -4.779 1.00 0.00 H >> ATOM 25 H5 -9.992 -17.547 -5.386 1.00 0.00H >> ATOM 26 H6 -9.692 -17.769 -2.991 1.00 0.00H >> ATOM 27 H7 -10.559 -16.076 -1.497 1.00 0.00 H >> ATOM 28 H8 -10.438 -15.123 -7.263 1.00 0.00 H >> ATOM 29 H9 -13.084 -16.397 -6.878 1.00 0.00 H >> ATOM 30 H10 -12.364 -15.825 -8.411 1.00 0.00 H >> >> >> Running PDB2gmx gives error as follows >> >
[gmx-users] Gromacs to AMBER
Hi all, Can any body know how to take Gromacs trajectories of protein ligand system to AMBER MM-PBSA and further calculate binding free energies using MM-PBSA.. Can any body suggest some tutorials..on this Cheers -- Sainitin D -- 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
Re: [gmx-users] Error in ligand coordinate file
Hi justin, Ok i will explain more clearly what i really have is protein ligand complex from Autodock..I choose best complex based on predicted binding affinity. Using pymol i visualized complex.pdb and saved only ligand (ligand.pdb given below) and used swiss param tool online http://swissparam.ch/ to charmm 27 FF .itp file then i followed tutorial and ran 10ns simulation now wanted to use g_lie to calculate binding free energies..of this complex..so have to run one more simulation for ligand only in water right...for that im using coordinate file which i have saved it from pymol in original PDB file it is properly aligned :) ATOM 1 C <1> d 83.432 21.209 56.133 -0.07 -0.02 C ATOM 2 C <1> d 84.828 21.291 56.786 -0.29 0.00 C ATOM 3 O <1> d 83.629 21.200 54.697 -0.02 -0.07 O ATOM 4 C <1> d 85.679 20.564 55.751 -0.19 -0.02 C ATOM 5 C <1> d 85.046 21.032 54.436 -0.15 0.04 C ATOM 6 N <1> d 82.546 22.305 56.532 -0.10 -0.05 N ATOM 7 C <1> d 81.884 22.186 57.757 0.18 0.05 C ATOM 8 N <1> d 81.028 23.185 58.155 0.01 -0.07 N ATOM 9 O <1> d 82.069 21.213 58.493 -0.09 0.04 O ATOM 10 C <1> d 80.868 24.232 57.405 -0.07 0.06 C ATOM 11 C <1> d 81.567 24.413 56.119 -0.49 0.00 C ATOM 12 C <1> d 82.377 23.424 55.745 -0.38 0.02 C ATOM 13 N <1> d 80.012 25.195 57.842 0.39 0.02 N ATOM 14 H <1> d 79.062 24.997 58.139 -0.05 -0.06 H ATOM 15 H <1> d 80.312 26.164 57.884 -0.11 -0.01 H ATOM 16 O <1> d 84.944 20.703 58.090 0.01 0.19 O ATOM 17 H <1> d 85.311 19.798 57.956 -0.17 -0.58 H ATOM 18 O <1> d 85.512 19.135 55.900 0.09 0.57 O ATOM 19 H <1> d 84.884 19.014 56.648 -0.30 -0.75 H ATOM 20 C <1> d 85.627 22.354 53.918 -0.22 0.11 C ATOM 21 O <1> d 84.597 23.194 53.394 -0.56 -0.44 O ATOM 22 H <1> d 83.757 22.697 53.521 0.27 0.18 H END Im running PDB2GMX to generate topol.top file..for this ligand by CHARMM 27 FF but it gives following error Fatal error: Residue '<1>' not found in residue topology database So now question how to solve this error..? Can you please suggest some help ? thanks, Nitin On Wed, Aug 8, 2012 at 12:08 PM, Justin Lemkul wrote: > > > On 8/8/12 5:37 AM, sai nitin wrote: >> >> Hi justin, >> >> Thanks for reply now i have ligand corrdinate file as follows >> >> ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N >> ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C >> ATOM 3 C A -13.037 -14.131 1.869 -0.32 -0.03 C >> ATOM 4 C A -12.284 -14.007 -0.761 -0.21 0.02 C >> ATOM 5 N A -11.897 -15.079 0.059 -0.24 -0.01 N >> ATOM 6 C A -12.288 -15.172 1.391 -0.37 0.01 C >> ATOM 7 N A -13.547 -13.886 3.036 -0.34 0.14 N >> ATOM 8 N A -14.076 -12.193 1.759 -0.27 0.01 N >> ATOM 9 C A -14.163 -12.729 2.956 -0.29 -0.08 C >> ATOM 10 N A -11.887 -13.919 -2.092 -0.05 0.04 N >> ATOM 11 H A -11.305 -15.802 -0.326 -0.11 -0.03 H >> ATOM 12 H A -12.027 -12.978 -2.454 -0.07 -0.16 H >> ATOM 13 C A -11.368 -14.845 -3.008 -0.39 0.00 C >> ATOM 14 C A -11.534 -14.731 -4.394 -0.49 0.00 C >> ATOM 15 C A -11.032 -15.710 -5.270 -0.32 0.00 C >> ATOM 16 C A -10.360 -16.822 -4.750 -0.24 0.00 C >> ATOM 17 C A -10.189 -16.950 -3.375 -0.33 0.00 C >> ATOM 18 C A -10.690 -15.970 -2.515 -0.42 0.00 C >> ATOM 19 C A -11.203 -15.559 -6.724 -0.27 0.00 C >> ATOM 20 C A -12.302 -15.958 -7.389 -0.19 0.02 C >> ATOM 21 O A -11.918 -16.240 2.152 -0.14 -0.09 O >> ATOM 22 H A -11.168 -16.702 1.710 -0.26 -0.13 H >> END >> >> Still not working >> >> Fatal error: >> Atom N in residue A 0 was not found i
Re: [gmx-users] Error in ligand coordinate file
Hi justin, Yes swiss param gave me ligand.itp file which gromacs topologies i included in topol.top file which i generated ..usign PDB2GMX so no need of creating seperate topol.top file for ligand only? can i use same topol.top file to run MD to simulate only ligand because current topol.top file has topologies for both ligand and protein.. Please help Nitin On Wed, Aug 8, 2012 at 5:10 PM, Justin Lemkul wrote: > > > On 8/8/12 10:44 AM, sai nitin wrote: >> >> Hi justin, >> >> Ok i will explain more clearly what i really have is protein ligand >> complex from Autodock..I choose best complex based on predicted >> binding affinity. Using pymol i visualized complex.pdb and saved only >> ligand (ligand.pdb given below) and used swiss param tool online >> http://swissparam.ch/ to charmm 27 FF .itp file then i followed >> tutorial and ran 10ns simulation now wanted to use g_lie to calculate >> binding free energies..of this complex..so have to run one more >> simulation for ligand only in water right...for that im using >> coordinate file which i have saved it from pymol >> in original PDB file it is properly aligned :) >> >> ATOM 1 C <1> d 83.432 21.209 56.133 -0.07 -0.02 >> C >> ATOM 2 C <1> d 84.828 21.291 56.786 -0.29 0.00 >> C >> ATOM 3 O <1> d 83.629 21.200 54.697 -0.02 -0.07 >> O >> ATOM 4 C <1> d 85.679 20.564 55.751 -0.19 -0.02 >> C >> ATOM 5 C <1> d 85.046 21.032 54.436 -0.15 0.04 >> C >> ATOM 6 N <1> d 82.546 22.305 56.532 -0.10 -0.05 >> N >> ATOM 7 C <1> d 81.884 22.186 57.757 0.18 0.05 >> C >> ATOM 8 N <1> d 81.028 23.185 58.155 0.01 -0.07 >> N >> ATOM 9 O <1> d 82.069 21.213 58.493 -0.09 0.04 >> O >> ATOM 10 C <1> d 80.868 24.232 57.405 -0.07 0.06 >> C >> ATOM 11 C <1> d 81.567 24.413 56.119 -0.49 0.00 >> C >> ATOM 12 C <1> d 82.377 23.424 55.745 -0.38 0.02 >> C >> ATOM 13 N <1> d 80.012 25.195 57.842 0.39 0.02 >> N >> ATOM 14 H <1> d 79.062 24.997 58.139 -0.05 -0.06 >> H >> ATOM 15 H <1> d 80.312 26.164 57.884 -0.11 -0.01 >> H >> ATOM 16 O <1> d 84.944 20.703 58.090 0.01 0.19 >> O >> ATOM 17 H <1> d 85.311 19.798 57.956 -0.17 -0.58 >> H >> ATOM 18 O <1> d 85.512 19.135 55.900 0.09 0.57 >> O >> ATOM 19 H <1> d 84.884 19.014 56.648 -0.30 -0.75 >> H >> ATOM 20 C <1> d 85.627 22.354 53.918 -0.22 0.11 >> C >> ATOM 21 O <1> d 84.597 23.194 53.394 -0.56 -0.44 >> O >> ATOM 22 H <1> d 83.757 22.697 53.521 0.27 0.18 >> H >> END >> >> Im running PDB2GMX to generate topol.top file..for this ligand by >> CHARMM 27 FF but it gives following error >> >> Fatal error: >> Residue '<1>' not found in residue topology database >> >> So now question how to solve this error..? Can you please suggest some >> help ? >> > > You say you used SwissParam, which should have given you a topology, > correct? If nothing else, it should have given you suitable parameters in > some form, after which you should follow what is described here: > > http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database > > pdb2gmx isn't magic. You need to tell it what all the ingredients are > before you expect it to produce a topology. > > > -Justin > > -- > > > 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 -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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] LIE calculations
Dear all, Recently i performed 10ns protein ligand simulation and also ran 10ns simulation only for ligand in solvent obtain parameters for g_lie to determine DGBind values. I calculated -Elj -Eqq values from ligand only simulation energy file... this is where im stuck :( -Elj = Lennard-Jones interaction between ligand and solvent -Eqq = Coulomb interaction between ligand and solvent Im not clear which energy terms should be taken for g_lie caluclation LJ-SR: LIG-rest or LJ-LR: LIG-rest or LJ-l4:LIG-rest for -Elj ?? Coul-SR:LIG-rest or Coul-l4 : LIG-rest for -Eqq ?? Can anybody please help Thanks, Nitin -- 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] LIE calculations
Dear all, Recently i performed 10ns protein ligand simulation and also ran 10ns simulation only for ligand in solvent obtain parameters for g_lie to determine DGBind values. I calculated -Elj -Eqq values from ligand only simulation energy file... this is where im stuck :( -Elj = Lennard-Jones interaction between ligand and solvent -Eqq = Coulomb interaction between ligand and solvent Im not clear which energy terms should be taken for g_lie caluclation LJ-SR: LIG-rest or LJ-LR: LIG-rest or LJ-l4:LIG-rest for -Elj ?? Coul-SR:LIG-rest or Coul-l4 : LIG-rest for -Eqq ?? Can anybody please help Thanks, Nitin -- -- 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] Problem during GROMACS 4.5.5 installation
Hi all, I just started learning molecular dynamics analysis of protein-ligand complexes to do this i downloaded GROMACS 4.5.5 and tried to install according to Manual instructions executed following commands.. ./configure make (when i executed this command it is showing following error *** No targets specified and no makefile found) Can any body help how to solved this... Thanks in advance -- Sainitin D -- 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] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
Hi, You can try swissparam online tool to generate protein and ligand topologies.. Cheers, Nitin On Wed, Nov 16, 2011 at 7:03 AM, arun kumar wrote: > hi justin, > > as u said i understand that there is inconsistency in the charges and > charge groups of PRODRG server itself. > can u suggest me any other softwares that i can rely on for this work. > > Thanking you. > > On Tue, Nov 15, 2011 at 7:48 PM, wrote: > >> Send gmx-users mailing list submissions to >>gmx-users@gromacs.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >>http://lists.gromacs.org/mailman/listinfo/gmx-users >> or, via email, send a message with subject or body 'help' to >>gmx-users-requ...@gromacs.org >> >> You can reach the person managing the list at >>gmx-users-ow...@gromacs.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gmx-users digest..." >> >> >> Today's Topics: >> >> 1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul) >> 2. RMSD (shahid nayeem) >> 3. Problem during GROMACS 4.5.5 installation (sai nitin) >> 4. Re: Problem during GROMACS 4.5.5 installation (Justin A. Lemkul) >> 5. Re: RMSD (Gianluca Santoni) >> 6. Re: RMSD (felmer...@uchile.cl) >> 7. Re: Positive potential energy for TFE solvent (Harpreet Basra) >> >> >> -- >> >> Message: 1 >> Date: Tue, 15 Nov 2011 06:40:31 -0500 >> From: "Justin A. Lemkul" >> Subject: Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION >> To: Discussion list for GROMACS users >> Message-ID: <4ec24faf.5050...@vt.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> >> arun kumar wrote: >> > Dear friends, >> > >> > i had a problem while running the of protein-ligand complex simulation, >> > in which i have generated the ligand toplogy by using online Prodrg >> > server and iam using gromos 96.1froce field. >> > >> > there was an note and an error during minimization >> > >> > NOTE 2 [file trp.top]: >> > The largest charge group contains 15 atoms. >> > Since atoms only see each other when the centers of geometry of the >> charge >> > groups they belong to are within the cut-off distance, too large >> charge >> > groups can lead to serious cut-off artifacts. >> > For efficiency and accuracy, charge group should consist of a few >> atoms. >> > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, >> etc. >> > >> > Analysing residue names: >> > There are: 223Protein residues >> > There are: 1 Other residues >> > There are: 25853 Water residues >> > Analysing Protein... >> > Analysing residues not classified as Protein/DNA/RNA/Water and splitting >> > into groups... >> > Number of degrees of freedom in T-Coupling group rest is 161838.00 >> > Largest charge group radii for Van der Waals: 0.790, 0.356 nm >> > Largest charge group radii for Coulomb: 0.790, 0.399 nm >> > >> > WARNING 1 [file em.mdp]: >> > The sum of the two largest charge group radii (1.188798) is larger >> than >> > rlist (1.00) >> > >> > i am using the mdp file the one that i copied from gromacs >> > protein-ligand tutorial >> > >> > can any one please explain these errors so that i can go farward in my >> work. >> > >> >> >> http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb >> >> > and i have a doubt, as there are other updated forcefields, how much >> > reliable is the gromos 96 ff >> > >> >> The problem is not the reliability of Gromos96, but the reliability of >> PRODRG. >> Please read the paper linked from >> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips to >> understand why >> you should almost certainly never use the charges and charge groups that >> PRODRG >> creates. >> >> -Justin >> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >>
Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
Hi arun, You can try swissparam online tool to generate protein and ligand topologies.. Cheers, Nitin -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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
