[gmx-users] Acetylation of lysine

[Justin Lemkul]

On 1/23/18 10:03 PM, Shraddha Parate wrote:
> 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

There is still the likelihood of something being misinterpreted here, or 
in any other file you've modified, if you're not using a proper 
plain-text editor. Never ignore formatting warnings.

>> 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 = ''

This error suggests your modifications to the .hdb file are incorrect, 
and are therefore not being used, so you get missing H atoms in KAC. 
Check your work, and again, always use a plain text editor.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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