[gmx-users] Gromacs error: equilibration phase

[Deep kumar]

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.choubey86 at 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 at 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
>