[gmx-users] (no subject)
Justin Lemkul
jalemkul at vt.edu
Thu Oct 19 23:07:04 CEST 2017
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.
> 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...
Don't ignore these - they mean you probably have missing residues in the
structure.
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 <jalemkul at 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 at 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 at 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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>>
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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