[gmx-users] Fwd:
I have performed a simulation for a protein-metal cluster complex system for 500ns. While calculating MMPBSA analysis for the system, I had selected two ranges of Trajectory period (100-110 ns; 290-300 ns) based on RMSD profile of protein-metal cluster 500 ns simulation period and executed the commands for a single range of trajectory period. In the result of the binding energy of my system, values are void. Hence, I Kindly need your valuable suggestions in this regard. Herewith I have attached the obtained results of my system, #Complex Number:1 === SUMMARY === van der Waal energy = -1144.250 +/- 28.405 kJ/mol Electrostattic energy= 0.000 +/-0.000 kJ/mol Polar solvation energy = nan +/- nan kJ/mol SASA energy = -25.841 +/-1.107 kJ/mol SAV energy = 0.000 +/-0.000 kJ/mol WCA energy = 0.000 +/-0.000 kJ/mol Binding energy = nan +/- nan kJ/mol === END === *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] (no subject)
Hello everyone, while running nvt equilibration i am getting the error as: Step 12, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms nan, max 92522.640625 (between atoms 217 and 218) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 277278 58.90.1090 74.2482 0.1090 281282 35.80.1098 73.5336 0.1090 281283 119.30.1097 74.0780 0.1090 281284 63.50.1097 74.2253 0.1090 step 12: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step12b.pdb to ./#step12b.pdb.1# Back Off! I just backed up step12c.pdb to ./#step12c.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) how can i resolve this error...? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] Fwd:
Hi users, I am performing a simulation for a protein-metal cluster complex system. I am trying to generate itp file for the metal cluster (Au) having 144 atoms. I have taken itp file of the metal cluster (Au) with ligand from an article(doi: 10.1016/j.colsurfa.2016.05.038) and extracted the parameters of metal clusters alone and I used it for my system preparation. During the energy minimization, Gromacs has shown errors like An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: ' '... Kindly need your valuable suggestions in this regard. With regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] (no subject)
Hi users, I have simulated a protein with gas molecules (CO2,NO2 and SO2) for 100ns. I have followed the protein ligand tutorial. I have applied position constraints. After equilibrium the gas molecules are at the docked position but at the 60ns simulation the gas molecules are far away from the protein. I have applied pBC and sure this is not an visualisatuin error. How can I rectify this, Kindly give your valuable suggestions in this regard. -- *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] (no subject)
Dear Users, My simulation system is Amyloid β Protein (1-42) with Fe2+ complex and i am using OPLSAA forcefield for the simulations. I edited the ffbonded.itp files accordingly as mentioned in the tutorials. While running grompp command, I get following error: gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr :-) GROMACS - gmx grompp, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, VERSION 5.1.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Setting the LD random seed to 2295799000 WARNING 1 [file ffnonbonded.itp, line 3]: Too few parameters on line (source file /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line 283) Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file c5.top, line 5912]: System has non-zero total charge: -2.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are:42Protein residues There are: 1 Other residues There are: 8015 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 49971.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113 Estimate for the relative computational load of the PME mesh part: 0.23 This run will generate roughly 2 Mb of data There was 1 note There was 1 warning --- Program gmx grompp, VERSION 5.1.2 Source code file: /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 2107 Fatal error: Too many warnings (1), gmx terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Anyone can help me in overcoming this fatal error will be appreciated. With Regards, Saranya Vasudevan, Research Scholar, Molecular Quantum Mechanics Laboratory, Department of Physics, Bharathiar University, Coimbatore-46 -- 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.
[gmx-users] (no subject)
Dear Users, I have done a simulation of Aggregated amyloid beta peptide for 100ns. The pdb structure choosen for my work is 1IYT, which has several (10) model structures, but i have choosen only 4 structure for my simulation. The problem is after production, if i check the final .gro files of md instead of 4 peptide structure i got only a single peptide structure. What is the reason for getting this result? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
Re: [gmx-users] Fwd:
Dear Justin, Thank you for your kind response. I have made all the basic analysis and yes there are certain structural changes that i have expected. But my clarification is as follows. Initially, there were 6 H-bonds and when it reach around 15ns it is reduced to 1 or 2. Do the effect of ligand over protein increase/decrease with a number of hydrogen bonds? Or even a single bond between protein and ligand is more sufficient to bring necessary changes to a protein? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] Fwd:
Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. The number of H-bond formation is very low I have a question about is there any influence of the drug in my protein? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
Re: [gmx-users] (no subject)
There is a minimum number of hydrogen bond formation (2 hydrogen bonds) in my protein-drug complex. I have a question about is there any influence of the drug in my protein-drug complex. -- 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.
[gmx-users] (no subject)
Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. I just want to clarify that 2 hydrogen bonds mean very low, is it acceptable to get this minimum number of bond formation for the protein drug interaction? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] (no subject)
Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. I just want to clarify that 2 hydrogen bonds mean very low, is it acceptable to get this minimum number of bond formation for the protein drug interaction? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
Re: [gmx-users] Gromacs
I have simulated the protein in water and protein with ligand for 100ns by using GPU and the edr file was generated using -rerun command on another system.I have just checked the pressure of my system by using gmx energy command, then i have selected pressure (group), but the calculated pressure is quite altered (20,000 pressure bar). Moreover, when I calculated the temperature of my system, the result was zero. I have used below mdp file for the calculation title = Protein-ligand complex NPT equilibration define = -DPOSRES_LIG ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 100 ps nstvout = 100 ; save velocities every 100 ps nstenergy = 100 ; save energies every 100 ps nstlog = 100 ; update log file every 100 ps energygrps = Protein ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_EPI Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; velocity generation off after NVT *With Regards,* *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] (no subject)
Hello sir, i want to extract the final pdb file for each ns, can you please explain how to extract the pdb files. With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] (no subject)
Hello sir, i want to extract the final pdb file for each ns, can you please explain how to extract the pdb files. With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
[gmx-users] (no subject)
Hello sir, i want to extract the final pdb file for each ns, can you please explain how to extract the pdb files. With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
Re: [gmx-users] Gromacs
i tried to run in OPLSAA force field sir. *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* On Tue, Oct 6, 2015 at 7:39 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > Maybe you should start telling is which force field you are trying to use. > GROMACS provides 15 different. > > Max > > > On Oct 6, 2015, at 1:51 AM, saranya <saranyahone...@gmail.com> wrote: > > > > GROMACS users, > > > > I was trying to perform a MD simulation of a system with a protein with > Ag+ > > metal ion but realized that GROMACS does not have parameters for the Ag+ > > ion. I tried to include the parameters in the ion.itp file but did not > > succeed yet. Does anyone knows the right procedure to introduce this ions > > into the file ions.itp? do we have to change anything more in order to > > GROMACS recognize the new ion? > > > > With Regards > > > > *Saranya Vasudevan,* > > > > *Research Scholar,* > > > > *Molecular Quantum Mechanics Laboratory,* > > > > *Department of Physics,* > > > > *Bharathiar University,* > > > > *Coimbatore-46* > > -- > > 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. > -- 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.
[gmx-users] (no subject)
GROMACS users, I was trying to perform a MD simulation of a system with a protein with Ag+ metal ion but realized that GROMACS does not have parameters for the Ag+ ion. I tried to include the parameters in the ion.itp file but did not succeed yet. Does anyone knows the right procedure to introduce this ions into the file ions.itp? do we have to change anything more in order to GROMACS recognize the new ion? *With Regards,* *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
Re: [gmx-users] Gromacs
GROMACS users, I was trying to perform a MD simulation of a system with a protein with Ag+ metal ion but realized that GROMACS does not have parameters for the Ag+ ion. I tried to include the parameters in the ion.itp file but did not succeed yet. Does anyone knows the right procedure to introduce this ions into the file ions.itp? do we have to change anything more in order to GROMACS recognize the new ion? With Regards *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
