<HTML><BODY>Dear Justin!<br><br>Sorry, HISE, not HIZE. <br><br>"<span style="color: #f82e00;" data-mce-style="color: #f82e00;">Will use HISE for residue 15" - <span style="color: rgb(0, 0, 0);">output from ..\src\gromacs\gmxpreprocess\hizzie.cpp, line 342</span></span><br><br>There is copy of cmdline output. <br><br><p>Microsoft Windows [Version 6.1.7601]<br>(c) Корпорация Майкрософт (Microsoft Corp.), 2009. Все права защищены.</p><p>C:\Users\BorisTimofeev>cd ..</p><p>C:\Users>cd ..</p><p>C:\>cd gromacs-2016</p><p>C:\gromacs-2016>cd mysamples</p><p>C:\gromacs-2016\mysamples>gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce<br> :-) GROMACS - gmx pdb2gmx, 2016 (-:</p><p>GROMACS is written by:<br> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar<br> Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof<br> Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis<br> Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson<br> Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund<br> Teemu Murtola Szilard Pall Sander Pronk Roland Schulz<br> Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman<br> Teemu Virolainen Christian Wennberg Maarten Wolf<br> and the project leaders:<br> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel</p><p>Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>Copyright (c) 2001-2015, The GROMACS development team at<br>Uppsala University, Stockholm University and<br>the Royal Institute of Technology, Sweden.<br>check out http://www.gromacs.org for more information.</p><p>GROMACS is free software; you can redistribute it and/or modify it<br>under the terms of the GNU Lesser General Public License<br>as published by the Free Software Foundation; either version 2.1<br>of the License, or (at your option) any later version.</p><p>GROMACS: gmx pdb2gmx, version 2016<br>Executable: C:\gromacs-2016\build\bin\Release\gmx.exe<br>Data prefix: C:\gromacs-2016 (source tree)<br>Working dir: C:\gromacs-2016\mysamples<br>Command line:<br> gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce</p><p><br>Select the Force Field:<br>From 'C:/gromacs-2016/share/top':<br> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)<br> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)<br> 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)<br> 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)<br> 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)<br> 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)<br> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)<br> 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)<br> 9: GROMOS96 43a1 force field<br>10: GROMOS96 43a2 force field (improved alkane dihedrals)<br>11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)<br>15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>15</p><p>Using the Oplsaa force field in directory oplsaa.ff</p><p>Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.r2b<br>Reading 1AKI.pdb...<br>WARNING: all CONECT records are ignored<br>Read 'LYSOZYME', 1079 atoms<br>Analyzing pdb file<br>Splitting chemical chains based on TER records or chain id changing.<br>There are 1 chains and 1 blocks of water and 207 residues with 1079 atoms</p><p>chain #res #atoms<br> 1 'A' 129 1001<br> 2 ' ' 78 78 (only water)</p><p><br>WARNING: there were 0 atoms with zero occupancy and 74 atoms with<br> occupancy unequal to one (out of 1079 atoms). Check your pdb file.</p><p>Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/atomtypes.atp<br>Atomtype 814<br>Reading residue database... (oplsaa)<br>Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.rtp<br>Residue 52<br>Sorting it all out...<br>Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.hdb<br>Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.n.tdb<br>Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.c.tdb</p><p>Back Off! I just backed up topol.top to ./#topol.top.4#<br>Processing chain 1 'A' (1001 atoms, 129 residues)<br>Analysing hydrogen-bonding network for automated assignment of histidine<br> protonation. 213 donors and 184 acceptors were found.<br>There are 255 hydrogen bonds<br><span style="color: rgb(248, 46, 0);">Will use HISE for residue 15</span><br>Identified residue LYS1 as a starting terminus.<br>Identified residue LEU129 as a ending terminus.<br>8 out of 8 lines of specbond.dat converted successfully<br>Special Atom Distance matrix:<br> CYS6 MET12 HIS15 CYS30 CYS64 CYS76 CYS80<br> SG48 SD87 NE2118 SG238 SG513 SG601 SG630<br> MET12 SD87 1.166<br> HIS15 NE2118 1.776 1.019<br> CYS30 SG238 1.406 1.054 2.069<br> CYS64 SG513 2.835 1.794 1.789 2.241<br> CYS76 SG601 2.704 1.551 1.468 2.116 0.765<br> CYS80 SG630 2.959 1.951 1.916 2.391 0.199 0.944<br> CYS94 SG724 2.550 1.407 1.382 1.975 0.665 0.202 0.855<br> MET105 SD799 1.827 0.911 1.683 0.888 1.849 1.461 2.036<br> CYS115 SG889 1.576 1.084 2.078 0.200 2.111 1.989 2.262<br> CYS127 SG981 0.197 1.072 1.721 1.313 2.799 2.622 2.934<br> CYS94 MET105 CYS115<br> SG724 SD799 SG889<br> MET105 SD799 1.381<br> CYS115 SG889 1.853 0.790<br> CYS127 SG981 2.475 1.686 1.483<br>Linking CYS-6 SG-48 and CYS-127 SG-981...<br>Linking CYS-30 SG-238 and CYS-115 SG-889...<br>Linking CYS-64 SG-513 and CYS-80 SG-630...<br>Linking CYS-76 SG-601 and CYS-94 SG-724...<br>Start terminus LYS-1: NH3+<br>End terminus LEU-129: COO-<br>Checking for duplicate atoms....<br>Generating any missing hydrogen atoms and/or adding termini.<br>Now there are 129 residues with 1960 atoms<br>Making bonds...<br>Number of bonds was 1984, now 1984<br>Generating angles, dihedrals and pairs...<br>Before cleaning: 5142 pairs<br>Before cleaning: 5187 dihedrals<br>Keeping all generated dihedrals<br>Making cmap torsions...<br>There are 5187 dihedrals, 426 impropers, 3547 angles<br> 5106 pairs, 1984 bonds and 0 virtual sites<br>Total mass 14313.193 a.m.u.<br><span style="background-color: rgb(255, 255, 255); color: rgb(248, 46, 0);">Total charge 7.887 e</span><br>Writing topology</p><p>Back Off! I just backed up posre.itp to ./#posre.itp.3#<br>Processing chain 2 (78 atoms, 78 residues)<br>Problem with chain definition, or missing terminal residues.<br>This chain does not appear to contain a recognized chain molecule.<br>If this is incorrect, you can edit residuetypes.dat to modify the behavior.<br>8 out of 8 lines of specbond.dat converted successfully<br>Checking for duplicate atoms....<br>Generating any missing hydrogen atoms and/or adding termini.<br>Now there are 78 residues with 234 atoms<br>Making bonds...<br>Number of bonds was 156, now 156<br>Generating angles, dihedrals and pairs...<br>Making cmap torsions...<br>There are 0 dihedrals, 0 impropers, 78 angles<br> 0 pairs, 156 bonds and 0 virtual sites<br>Total mass 1405.201 a.m.u.<br>Total charge 0.000 e<br>Including chain 1 in system: 1960 atoms 129 residues<br>Including chain 2 in system: 234 atoms 78 residues<br>Now there are 2194 atoms and 207 residues<br>Total mass in system 15718.394 a.m.u.<br>Total charge in system 7.887 e</p><p>Writing coordinate file...</p><p>Back Off! I just backed up 1AKI_processed.gro to ./#1AKI_processed.gro.2#<br> --------- PLEASE NOTE ------------<br>You have successfully generated a topology from: 1AKI.pdb.<br>The Oplsaa force field and the spce water model are used.<br> --------- ETON ESAELP ------------</p><p>GROMACS reminds you: "If I Were You I Would Give Me a Break" (F. Black)</p><br>From file topol.top: qtot <br><br><p>227 opls_235 14 ARG C 74 0.5 12.011 ; qtot 4.5<br> 228 opls_236 14 ARG O 74 -0.5 15.9994 ; qtot 4<br>; residue 15 HIS rtp HISE q -0.1<br> 229 opls_238 15 HIS N 75 -0.5 14.0067 ; qtot 3.5<br> 230 opls_241 15 HIS H 75 0.3 1.008 ; qtot 3.8<br> 231 opls_224B 15 HIS CA 75 0.14 12.011 ; qtot 3.94<br> 232 opls_140 15 HIS HA 75 0.06 1.008 ; qtot 4<br> 233 opls_505 15 HIS CB 76 -0.005 12.011 ; qtot 3.995<br> 234 opls_140 15 HIS HB1 76 0.06 1.008 ; qtot 4.055<br> 235 opls_140 15 HIS HB2 76 0.06 1.008 ; qtot 4.115<br> 236 opls_507 15 HIS CG 77 -0.015 12.011 ; qtot 4.1<br> 237 opls_511 15 HIS ND1 77 -0.49 14.0067 ; qtot 3.61<br> 238 opls_508 15 HIS CD2 78 0.015 12.011 ; qtot 3.625<br> 239 opls_146 15 HIS HD2 78 0.115 1.008 ; qtot 3.74<br> 240 opls_506 15 HIS CE1 79 0.182 12.011 ; qtot 3.922<br> 241 opls_146 15 HIS HE1 79 0.115 1.008 ; qtot 4.037<br> 242 opls_503 15 HIS NE2 80 -0.57 14.0067 ; qtot 3.467<br> 243 opls_504 15 HIS HE2 80 0.42 1.008 ; qtot 3.887<br> 244 opls_235 15 HIS C 81 0.5 12.011 ; qtot 4.387<br> 245 opls_236 15 HIS O 81 -0.5 15.9994 ; qtot 3.887<br>; residue 16 GLY rtp GLY q 0.0<br> 246 opls_238 16 GLY N 82 -0.5 14.0067 ; qtot 3.387<br> 247 opls_241 16 GLY H 82 0.3 1.008 ; qtot 3.687</p><br><br><br><br><br><br><blockquote style="border-left:1px solid #0857A6; margin:10px; padding:0 0 0 10px;">
Понедельник, 3 октября 2016, 1:01 +03:00 от Justin Lemkul <jalemkul@vt.edu>:<br>
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On 10/2/16 5:42 PM, Boris Timofeev wrote:<br>
><br>
> Good afternoon to all!<br>
><br>
> I did a great job on compilation of the "portable" Gromacs-2016 version on the<br>
> Win64 platform without cygwin with OpenCL support and AVX_256/AVX2_256<br>
> expansions. The project is builded on VS-2015. By small changes in CMakeLists, I<br>
> managed to achieve that both the "embedded" tests, and regressiontests, are<br>
> executed after assembly immediately from VS IDE. It was tested on Windows7/<br>
> Windows10 with IntelCore i3, i5, i7 processors and video cards from Nvidia and<br>
> AMD. So far it was not succeeded to win - against the video card from Intel -<br>
> Intel OpenCL compiler preprocessor is left unfinished, does not recognize<br>
> directive "-I" and have buggy concatention (##) implementation.<br>
> It was necessary to realize a primitive preprocessor, became successful, but<br>
> all the same calculations (tests and regressiontests) are wrong as it was<br>
> already metioned here (https://bugs.freedesktop.org/show_bug.cgi?<br>
> id=94265#add_comment).<br>
><br>
> If it is interesting to community, I am ready to report about some necessary<br>
> changes in progect and to provide the main CMake-file.<br>
><br>
> There are several questions to developers.<br>
><br>
> 1. The nbnxn_ocl_kernel_nvidia.clh, nbnxn_ocl_kernel_nowarp.clh and<br>
> nbnxn_ocl_kernel_amd.clh files, if to compare their with kdiff, differ only in<br>
> comments and lack of unroll pragma for Nvidia. Why not to unite them in one?<br>
> Where the promised optimization?<br>
><br>
> 2. Why in the Gromacs'a code so many paths to files are embedded up? To start<br>
> tests without development environment on other computer it is necessary to copy<br>
> practically all project.<br>
><br>
> 3. A question "on science". When performing an example of<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html</a>,<br>
> pdb2gmx for the aminoacid residue HIS ("HIZE-branch" on stdout ), unlike all<br>
> others residue, gives a nonintegral charge 0.883, inexplicable with round-off<br>
> errors.<br>
> Whether there is no program mistake here?<br>
><br>
<br>
I can't speak to points 1 and 2, but here: what is HIZE-branch? I've never <br>
heard of that. Note, too, that if you're working with a single amino acid with <br>
OPLS-AA, you can't rely on the default terminus selection. You need to choose <br>
the zwitterion termini, otherwise the charges will be junk because OPLS-AA makes <br>
changes to CA depending on whether the residue is a zwitterion or in a polypeptide.<br>
<br>
-Justin<br>
<br>
-- <br>
==================================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br>
<br>
Department of Pharmaceutical Sciences<br>
School of Pharmacy<br>
Health Sciences Facility II, Room 629<br>
University of Maryland, Baltimore<br>
20 Penn St.<br>
Baltimore, MD 21201<br>
<br>
<a href="mailto:jalemkul@outerbanks.umaryland.edu">jalemkul@outerbanks.umaryland.edu</a> | (410) 706-7441<br>
<a href="http://mackerell.umaryland.edu/~jalemkul" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br>
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