Dear All, I have produced the "ITP" files of the ligands using ATB server. I am mentioning the steps here, please let me know if you think anything is wrong.
a) uploaded the coordinates of ligand "RND" on ATB server. I chose "heteromoelcule" molecule type. b) Entered the "net charge" by calculating like this using chimera: (added Hydrogen prior to calculating net charge and produced .mol2 file to calculate the net charge) from chimera import openModels, Molecule from AddCharge import estimateNetCharge from OpenSave import osOpen output = osOpen("charge-estimates", "w") for m in openModels.list(modelTypes=[Molecule]): print>>output, m, m.name, estimateNetCharge(m.atoms) output.close() the "net charge" of "RND" was shown to be "2". c) submitted the entry and after completion, downloaded the file as below: >From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7" & "Format" to be "Gromacs", and downloaded "All Atom" ITP file. I am running the MD on Gromacs version 5.1. I have prepared the protein topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field. Please let me know if I did right or if anything else is needed to be done. Secondly, I also need .gro file of the ligand. Can you please let me know how can I get that. The tutorial am following ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I have to prepare a position restraint file "posre_RND.itp" from the "RND.gro" file, so how can I get the "RND.gro" file? Thanks, Deep On Tue, Sep 5, 2017 at 4:04 PM, Deep kumar <deepak.choube...@gmail.com> wrote: > Dear All, > > I have a query regarding Gromacs run. The error when running the > "equilibration phase". I am following the tutorial from here: > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/complex/06_equil.html > <https://www.researchgate.net/deref/http%3A%2F%2Fwww.bevanlab.biochem.vt.edu%2FPages%2FPersonal%2Fjustin%2Fgmx-tutorials%2Fcomplex%2F06_equil.html> > > I am trying to prepare a system for MD run of 20ns for the pdb "4NYM". For > the same I prepared two pdb files; 4NYM_clean.pdb (without ligands, > GNP[ligand2.pdb] & RND[ligand3.pdb]) & 4NYM.pdb (with ligands). I produced > the .itp and .gro files of the ligands separately using "prodrg" > (attached). "posre_GNP.itp" & "posre_RND.itp" files were produced using > gromacs tutorial by "gmx genrestr". All steps went well without error until > the "nvt.mdp" equilibration run. I have attached the pdb files and the .mdp > files I used. I have also attached a produced pdb (step0c.pdb) file just > before the "nvt" crash/error. > > minim.mdp: is the file used to get "ions.tpr" > em_real.mdp: for energy minimization > nvt.mdp: for first equilibration phase > > The error I get is: > > [root@g ras-sos]# gmx mdrun -deffnm nvt > > :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar > > Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch > > Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen > > Dimitrios Karkoulis Peter Kasson Jiri 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 Tieleman Teemu Virolainen Christian Wennberg Maarten 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 > <https://www.researchgate.net/deref/http%3A%2F%2Fwww.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 mdrun, VERSION 5.1.4 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Command line: > > gmx mdrun -deffnm nvt > > > > > > Back Off! I just backed up nvt.log to ./#nvt.log.6# > > > > Running on 1 node with total 4 cores, 4 logical cores > > Hardware detected: > > CPU info: > > Vendor: GenuineIntel > > Brand: Intel(R) Xeon(R) CPU E3-1220 v3 @ 3.10GHz > > SIMD instructions most likely to fit this hardware: AVX2_256 > > SIMD instructions selected at GROMACS compile time: AVX2_256 > > > > Reading file nvt.tpr, VERSION 5.1.4 (single precision) > > Changing nstlist from 10 to 25, rlist from 1.4 to 1.433 > > > > Using 1 MPI thread > > Using 4 OpenMP threads > > > > > > Back Off! I just backed up nvt.trr to ./#nvt.trr.6# > > > > Back Off! I just backed up nvt.edr to ./#nvt.edr.6# > > > > Step 0, time 0 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 0.001552, max 0.079199 (between atoms 6653 and 6655) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > starting mdrun 'Protein in water' > > 50000 steps, 100.0 ps. > > > > Step 0, time 0 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 51.089629, max 2377.131592 (between atoms 6655 and 6656) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 6643 6644 60.0 0.1015 0.1606 0.1000 > > 6643 6645 130.6 0.1543 0.6547 0.1470 > > 6645 6646 150.2 0.1589 0.6682 0.1530 > > 6645 6653 71.6 0.1544 4.6055 0.1530 > > 6646 6647 33.8 0.1548 0.3257 0.1530 > > 6653 6654 79.0 0.1219 4.5065 0.1230 > > 6653 6655 63.7 0.1435 244.5352 0.1330 > > 6655 6656 161.7 0.0996 237.8132 0.1000 > > 6655 6657 115.4 0.1526 239.9015 0.1470 > > 6657 6658 149.5 0.1591 0.3734 0.1530 > > 6657 6662 99.9 0.1600 0.1708 0.1530 > > 6658 6659 82.2 0.1444 0.4133 0.1430 > > 6658 6661 67.3 0.1543 0.4097 0.1530 > > 6659 6660 42.1 0.1002 0.1383 0.1000 > > 6662 6663 46.8 0.1249 0.1680 0.1230 > > 6662 6664 70.9 0.1352 0.1831 0.1330 > > 6664 6665 34.8 0.1007 0.1286 0.1000 > > 8431 8428 78.4 0.1475 0.1388 0.1470 > > 8431 8430 72.3 0.1475 0.1352 0.1470 > > 8431 8432 88.2 0.1004 0.1727 0.1000 > > 8431 8433 94.5 0.1493 0.7373 0.1470 > > 8434 8433 86.0 0.1552 2.9414 0.1530 > > 8434 8435 89.4 0.1376 3.8582 0.1330 > > 8434 8447 89.9 0.1345 3.8510 0.1330 > > 8435 8436 74.2 0.1352 0.8889 0.1330 > > 8435 8444 87.8 0.1343 4.3500 0.1330 > > 8438 8439 56.8 0.1096 0.1229 0.1090 > > 8438 8440 78.0 0.1397 0.4233 0.1390 > > 8440 8441 72.6 0.1095 0.2804 0.1090 > > 8440 8442 85.6 0.1407 1.1677 0.1390 > > 8442 8443 82.6 0.1105 0.7768 0.1090 > > 8444 8442 85.8 0.1343 3.7720 0.1330 > > 8444 8445 50.9 0.1343 214.2921 0.1330 > > 8445 8446 144.6 0.1008 225.9639 0.1000 > > 8445 8447 61.9 0.1335 231.1140 0.1330 > > 8447 8448 89.0 0.1098 4.3652 0.1090 > > > > Back Off! I just backed up step0b.pdb to ./#step0b.pdb.6# > > > > Back Off! I just backed up step0c.pdb to ./#step0c.pdb.6# > > Wrote pdb files with previous and current coordinates > > > > WARNING: Listed nonbonded interaction between particles 6643 and 6655 > > at distance 240.162 which is larger than the table limit 21.433 nm. > > > > This is likely either a 1,4 interaction, or a listed interaction inside > > a smaller molecule you are decoupling during a free energy calculation. > > Since interactions at distances beyond the table cannot be computed, > > they are skipped until they are inside the table limit again. You will > > only see this message once, even if it occurs for several interactions. > > > > IMPORTANT: This should not happen in a stable simulation, so there is > > probably something wrong with your system. Only change the table-extension > > distance in the mdp file if you are really sure that is the reason. > > Segmentation fault (core dumped) > > > I tried using low timesteps but that also did not solve the problem. I > have also attached the "topol.top" file. I would really appreciate your > help to understand and solve the problem. Please let me know if I need to > provide any further information. Thanks much for your time. > > Regards, > Dipak > -- 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.