Yeah! But I don't want any charge at terminal residues. I think I should cap these by acetyl or amide moiety. Let me try this.
On Fri, 6 Sep 2019, 19:45 Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 9/6/19 4:32 AM, Navneet Kumar Singh wrote: > > Hello Everyone! > > > > I am trying to simulate five peptides along with water using GROMACS. > > I have used the PACKMOL to prepare initail PDB files. > > Peptide were made using Schrodinger Maestro. > > I have got a final PDB file having the water molecules and randowmly > > distributed peptides. > > > > > > After that I am using command pdb2gmx using the CHARMM36 force field. > > > > Following are the commands and its output, > > > > > ------------------------------------------------------------------------------------------------------------- > > gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter > > :-) GROMACS - gmx pdb2gmx, 2018.4 (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > > Berendsen > > Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton > Feenstra > > Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca > Hamuraru > > Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri > Kraus > > > > Carsten Kutzner Per Larsson Justin A. Lemkul Viveca > Lindahl > > 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) 2001-2017, 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 pdb2gmx, version 2018.4 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Working dir: /home/navneet/Desktop/amyloid > > Command line: > > gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter > > > > > > Select the Force Field: > > From current directory: > > 1: CHARMM36 all-atom force field (March 2019) > > From '/usr/local/gromacs/share/gromacs/top': > > 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, > > 1999-2012, 2003) > > 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) > > 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. > 29, > > 461-469, 1996) > > 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, > > 1049-1074, 2000) > > 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, > > 712-725, 2006) > > 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., > > Proteins 78, 1950-58, 2010) > > 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) > > 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) > > 10: GROMOS96 43a1 force field > > 11: GROMOS96 43a2 force field (improved alkane dihedrals) > > 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) > > 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) > > 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) > > 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, > DOI: > > 10.1007/s00249-011-0700-9) > > 16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, > DOI: > > 10.1007/s00249-011-0700-9) > > 17: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, > DOI: > > 10.1007/s00249-011-0700-9) > > 18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) > > 1 > > > > Using the Charmm36-mar2019 force field in directory ./charmm36-mar2019.ff > > > > Opening force field file ./charmm36-mar2019.ff/merged.r2b > > Reading final.pdb... > > Read 'Built with Packmol through Packmol Memgen', 5305 atoms > > Analyzing pdb file > > Splitting chemical chains based on TER records or chain id changing. > > There are 1 chains and 1 blocks of water and 5035 residues with 5305 > atoms > > > > chain #res #atoms > > 1 'A' 35 305 > > 2 ' ' 5000 5000 (only water) > > > > > > WARNING: there were 5000 atoms with zero occupancy and 0 atoms with > > occupancy unequal to one (out of 5305 atoms). Check your pdb > file. > > > > Opening force field file ./charmm36-mar2019.ff/atomtypes.atp > > Atomtype 447 > > Reading residue database... (charmm36-mar2019) > > Opening force field file ./charmm36-mar2019.ff/merged.rtp > > Residue 1318 > > Sorting it all out... > > Opening force field file ./charmm36-mar2019.ff/merged.hdb > > Opening force field file ./charmm36-mar2019.ff/merged.n.tdb > > Opening force field file ./charmm36-mar2019.ff/merged.c.tdb > > > > Back Off! I just backed up topol.top to ./#topol.top.2# > > Processing chain 1 'A' (305 atoms, 35 residues) > > Identified residue LYS1 as a starting terminus. > > Identified residue GLU7 as a ending terminus. > > 8 out of 8 lines of specbond.dat converted successfully > > Select start terminus type for LYS-1 > > 0: NH3+ > > 1: NH2 > > 2: 5TER > > 3: None > > 1 > > Start terminus LYS-1: NH2 > > Select end terminus type for GLU-7 > > 0: COO- > > 1: COOH > > 2: CT2 > > 3: 3TER > > 4: None > > 1 > > End terminus GLU-7: COOH > > These are curious choices; there is no pH value at which both termini > will be in their neutral forms. You may wish to reconsider what > chemistry you're assigning. > > > Opening force field file ./charmm36-mar2019.ff/merged.arn > > > > ------------------------------------------------------- > > Program: gmx pdb2gmx, version 2018.4 > > Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753) > > > > Fatal error: > > Atom O4 in residue GLU 7 was not found in rtp entry GLU with 15 atoms > > while sorting atoms. > > . > > Check your input coordinate file because apparently the atom names do > not use standard nomenclature. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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