[gmx-users] Acetylation of lysine
Shraddha Parate
parateshraddha at gmail.com
Wed Jan 24 04:03:47 CET 2018
On Wed, Jan 24, 2018 at 11:58 AM, Shraddha Parate <parateshraddha at gmail.com>
wrote:
> [sp at atp 2RTU_Gromos45a3]$ gmx pdb2gmx -f 2RTU_1.pdb -o 2RTU.gro -water
> spce
> GROMACS: gmx pdb2gmx, VERSION 5.0.6
>
> 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 Peter Kasson 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 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) 2001-2014, 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 5.0.6
> Executable: /usr/local/gromacs_5.0.6/bin/gmx
> Library dir: /usr/local/gromacs_5.0.6/share/gromacs/top
> Command line:
> gmx pdb2gmx -f 2RTU_1.pdb -o 2RTU.gro -water spce
>
>
> Select the Force Field:
> From current directory:
> 1: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> From '/usr/local/gromacs_5.0.6/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 53A6 force field, extended to include Berger lipid parameters
> 16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
> 10.1007/s00249-011-0700-9)
> 17: gromos_lipid
> 18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 1
>
> Using the Gromos45a3 force field in directory ./gromos45a3.ff
>
> Warning: file does not end with a newline, last line:
> KAC Protein
> Opening force field file ./gromos45a3.ff/aminoacids.r2b
> Warning: file does not end with a newline, last line:
> KAC Protein
> Reading 2RTU_1.pdb...
> WARNING: all CONECT records are ignored
> Read 715 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 87 residues with 715 atoms
>
> chain #res #atoms
> 1 'A' 87 715
>
> All occupancies are one
> Opening force field file ./gromos45a3.ff/atomtypes.atp
> Atomtype 49
> Reading residue database... (gromos45a3)
> Opening force field file ./gromos45a3.ff/aminoacids.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing proper dihedrals found on the same bond as a
> proper dihedral
> Residue 97
> Sorting it all out...
> Opening force field file ./gromos45a3.ff/aminoacids.hdb
> Error in hdb file: nah = 44
> line = ''
> Opening force field file ./gromos45a3.ff/aminoacids.n.tdb
> Opening force field file ./gromos45a3.ff/aminoacids.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.1#
> Processing chain 1 'A' (715 atoms, 87 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
> protonation. 142 donors and 130 acceptors were found.
> There are 161 hydrogen bonds
> Will use HISE for residue 3
> Will use HISE for residue 30
> Will use HISE for residue 34
> Identified residue GLY1 as a starting terminus.
> Identified residue GLU87 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> HIS3 MET4 MET16 CYS26 HIS30 HIS34 CYS48
> NE220 SD27 SD116 SG197 NE2236 NE2282 SG390
> MET4 SD27 1.094
> MET16 SD116 2.562 1.737
> CYS26 SG197 3.082 2.541 1.196
> HIS30 NE2236 3.594 3.072 1.997 1.062
> HIS34 NE2282 4.103 3.549 2.430 1.525 0.537
> CYS48 SG390 2.983 2.489 1.279 0.203 0.989 1.486
> MET55 SD453 3.442 3.024 1.636 0.812 1.679 2.055 0.910
> MET66 SD540 3.534 2.808 1.100 1.204 2.076 2.390 1.397
> MET78 SD641 2.579 1.841 1.819 2.951 3.808 4.243 3.025
> MET55 MET66
> SD453 SD540
> MET66 SD540 1.175
> MET78 SD641 3.124 2.406
> Linking CYS-26 SG-197 and CYS-48 SG-390...
> Start terminus GLY-1: GLY-NH3+
> End terminus GLU-87: COO-
> Checking for duplicate atoms....
> Now there are 714 atoms. Deleted 1 duplicates.
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 87 residues with 927 atoms
> Warning: file does not end with a newline, last line:
> KAC Protein
>
> Making bonds...
>
> WARNING: atom H is missing in residue KAC 31 in the pdb file
> You might need to add atom H to the hydrogen database of building
> block KAC
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HZ is missing in residue KAC 31 in the pdb file
> You might need to add atom HZ to the hydrogen database of
> building block KAC
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom H is missing in residue KAC 32 in the pdb file
> You might need to add atom H to the hydrogen database of building
> block KAC
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HZ is missing in residue KAC 32 in the pdb file
> You might need to add atom HZ to the hydrogen database of
> building block KAC
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom H is missing in residue KAC 33 in the pdb file
> You might need to add atom H to the hydrogen database of building
> block KAC
> in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HZ is missing in residue KAC 33 in the pdb file
> You might need to add atom HZ to the hydrogen database of
> building block KAC
> in the file aminoacids.hdb (see the manual)
>
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.6
> Source code file: /home/users/cbbl/gromacs-5.0.6
> /src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1587
>
> Fatal error:
> There were 6 missing atoms in molecule Protein_chain_A, if you want to use
> this incomplete topology anyhow, use the option -missing
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> These are my working directory files
>
(
http://i1339.photobucket.com/albums/o711/Shrads_90/Capture1_zpsh0qa22hn.png)
>
> And this is KAC defined as Protein in residuetypes.dat file:
> (
> http://i1339.photobucket.com/albums/o711/Shrads_90/Capture2_zpsye0jwtjd.png
> )
>
> Please help me in knowing where I am going wrong.
>
> Thanks in advance,
>
> Shraddha
>
--
More information about the gromacs.org_gmx-users
mailing list