On 10/19/17 11:30 AM, Robert Nairn wrote:
Yes I noticed the area per protein was displaying 0 from the output on the terminal. Having repeated the tutorial with my protein, i consistently get two messages that could be responsible. If i try to select start terminus as none (2) as per the tutorial I receive a message saying:
The tutorial chooses no terminal patching because I already built on capping groups (acetyl and amide) to both termini. If this is not the case in your system, it's not an appropriate choice.
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (4756 atoms, 625 residues)
Identified residue MET1 as a starting terminus.
Identified residue ASN625 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 MET126 MET251 MET376
SD5 SD956 SD1907 SD2858
MET126 SD956 3.533
MET251 SD1907 5.410 3.187
MET376 SD2858 5.451 5.516 3.535
MET501 SD3809 3.427 5.522 5.366 3.172
Select start terminus type for MET-1
0: NH3+
1: NH2
2: None
2
Start terminus MET-1: None
Select end terminus type for ASN-625
0: COO-
1: COOH
2: None
2
End terminus ASN-625: None
-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1.4
Source code file:
/usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1088
Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Alternatively I've used uncharged terminal end (1) for NH2 and COOH and get
this warning:
Processing chain 1 (4756 atoms, 625 residues)
Identified residue MET1 as a starting terminus.
Identified residue ASN625 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 MET126 MET251 MET376
SD5 SD956 SD1907 SD2858
MET126 SD956 3.533
MET251 SD1907 5.410 3.187
MET376 SD2858 5.451 5.516 3.535
MET501 SD3809 3.427 5.522 5.366 3.172
Select start terminus type for MET-1
0: NH3+
1: NH2
2: None
1
Start terminus MET-1: NH2
Select end terminus type for ASN-625
0: COO-
1: COOH
2: None
1
End terminus ASN-625: COOH
That's chemically impossible but at least it's a syntactically correct choice.
Don't ignore these - they mean you probably have missing residues in the structure.Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 625 residues with 6003 atoms Making bonds... Warning: Long Bond (1200-1202 = 5.44802 nm) Warning: Long Bond (2400-2402 = 5.45768 nm) Warning: Long Bond (3600-3602 = 5.21815 nm) Warning: Long Bond (4800-4802 = 5.51416 nm) Number of bonds was 6071, now 6067 Generating angles, dihedrals and pairs...
I'm not sure any of the above is in any way related to the InflateGRO failure (and really, without the coordinate file itself, there's not much to go on) but you have plenty to consider about how reasonable your starting system is.
-Justin
WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. I've looked through the pdb input files and the .gro output files and can't find and erroneous hydrogen atoms, I've also been sure to change all HW atom types to H. I'm unsure if this is where my problem lies... Thanks, Robert On 19 October 2017 at 10:55, Justin Lemkul <jalem...@vt.edu> wrote:On 10/19/17 8:04 AM, Robert Nairn wrote:Dear all, I am currently trying to insert the MscL protein into the DMPC bilayer. I followed Justin Lemkul's tutorial 2 (with the exception of using dmpc instead of dppc) and receive this error message after shrinking and energy minimization. [christos@chpc-cp39 Simulation]$ gmx mdrun -v -deffnm em :-) 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 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 -v -deffnm em Back Off! I just backed up em.log to ./#em.log.7# Running on 1 node with total 4 cores, 4 logical cores Hardware detected: CPU info: Vendor: GenuineIntel Brand: Intel(R) Core(TM) i5-4460 CPU @ 3.20GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 Reading file em.tpr, VERSION 5.1.4 (single precision) Using 1 MPI thread Using 4 OpenMP threads Back Off! I just backed up em.trr to ./#em.trr.7# Back Off! I just backed up em.edr to ./#em.edr.7# Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= -3.20786e+05 Fmax= 1.71766e+03, atom= 328 Step= 2, Dmax= 5.0e-03 nm, Epot= -3.22206e+05 Fmax= 2.42847e+03, atom= 5581 Step= 3, Dmax= 6.0e-03 nm, Epot= -3.22537e+05 Fmax= 5.33224e+03, atom= 5581 Step= 4, Dmax= 7.2e-03 nm, Epot= -3.23803e+05 Fmax= 3.73628e+03, atom= 5581 Step= 6, Dmax= 4.3e-03 nm, Epot= -3.24377e+05 Fmax= 1.77965e+03, atom= 5581 Step= 7, Dmax= 5.2e-03 nm, Epot= -3.24696e+05 Fmax= 4.72325e+03, atom= 5581 Step= 8, Dmax= 6.2e-03 nm, Epot= -3.25203e+05 Fmax= 3.21307e+03, atom= 5581 Step= 10, Dmax= 3.7e-03 nm, Epot= -3.25578e+05 Fmax= 1.53786e+03, atom= 5581 Step= 11, Dmax= 4.5e-03 nm, Epot= -3.25794e+05 Fmax= 4.19745e+03, atom= 5581 Step= 12, Dmax= 5.4e-03 nm, Epot= -3.26199e+05 Fmax= 2.65229e+03, atom= 5581 Step= 14, Dmax= 3.2e-03 nm, Epot= -3.26475e+05 Fmax= 1.44458e+03, atom= 5581 Step= 15, Dmax= 3.9e-03 nm, Epot= -3.26646e+05 Fmax= 3.51711e+03, atom= 889 Step= 16, Dmax= 4.6e-03 nm, Epot= -3.26945e+05 Fmax= 2.42357e+03, atom= 889 Step= 18, Dmax= 2.8e-03 nm, Epot= -3.27174e+05 Fmax= 1.16101e+03, atom= 889 Step= 19, Dmax= 3.3e-03 nm, Epot= -3.27357e+05 Fmax= 3.10626e+03, atom= 889 Step= 20, Dmax= 4.0e-03 nm, Epot= -3.27599e+05 Fmax= 2.04763e+03, atom= 889 Step= 21, Dmax= 4.8e-03 nm, Epot= -3.27618e+05 Fmax= 4.11224e+03, atom= 889 Step= 22, Dmax= 5.8e-03 nm, Epot= -3.27866e+05 Fmax= 3.29947e+03, atom= 889 Step= 24, Dmax= 3.5e-03 nm, Epot= -3.28131e+05 Fmax= 1.11942e+03, atom= 889 Step= 25, Dmax= 4.2e-03 nm, Epot= -3.28185e+05 Fmax= 4.23073e+03, atom= 889 Step= 26, Dmax= 5.0e-03 nm, Epot= -3.28509e+05 Fmax= 2.13723e+03, atom= 889 Step= 28, Dmax= 3.0e-03 nm, Epot= -3.28653e+05 Fmax= 1.71455e+03, atom= 889 Step= 29, Dmax= 3.6e-03 nm, Epot= -3.28732e+05 Fmax= 2.86474e+03, atom= 889 Step= 30, Dmax= 4.3e-03 nm, Epot= -3.28867e+05 Fmax= 2.67060e+03, atom= 889 Step= 31, Dmax= 5.2e-03 nm, Epot= -3.28877e+05 Fmax= 3.93851e+03, atom= 889 Step= 32, Dmax= 6.2e-03 nm, Epot= -3.28983e+05 Fmax= 4.01820e+03, atom= 889 Step= 34, Dmax= 3.7e-03 nm, Epot= -3.29290e+05 Fmax= 7.22653e+02, atom= 889 writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.7# Steepest Descents converged to Fmax < 1000 in 35 steps Potential Energy = -3.2929012e+05 Maximum force = 7.2265314e+02 on atom 889 Norm of force = 7.2922180e+01 NOTE: 20 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) gcq#490: "I have a hunch that the unknown sequences of DNA will decode into copyright notices and patent protections." (Donald Knuth) [christos@chpc-cp39 Simulation]$ perl inflategro.pl em.gro 0.95 DMPC 0 system_shrink1.gro 5 area_shrink1.dat Reading..... Scaling lipids.... There are 128 lipids... with 46 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet No protein coordinates found...This line is key - make sure you have what you think you have (e.g. you didn't accidentally just minimize a bilayer with no protein or something). -Justin Writing scaled bilayer & centered protein...Calculating Area per lipid... Protein X-min/max: 10000 -9999 Protein Y-min/max: 10000 -9999 X-range: -19999 A Y-range: -19999 A Building -19999 X -19999 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD.. lower TMD.. Area per protein: 0 nm^2 Area per lipid: 0.53787556 nm^2 Area per protein, upper half: 0 nm^2 Area per lipid, upper leaflet : 0.53787556 nm^2 Area per protein, lower half: 0 nm^2 Area per lipid, lower leaflet : 0.53787556 nm^2 Writing Area per lipid... Done! I've also tried the same process with popc and dppc and get the same error message. I've previously read that it could be an issue with the grompp coordinate input file, but I'm not sure what is wrong in this instance. Best, Robert-- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
-- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
