[gmx-users] Acetylation of lysine
Shraddha Parate
parateshraddha at gmail.com
Wed Jan 24 03:58:47 CET 2018
[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
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Copyright (c) 2001-2014, The GROMACS development team at
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check out http://www.gromacs.org for more information.
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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 ([URL=
http://s1339.photobucket.com/user/Shrads_90/media/Capture1_zpsgszdjsk8.png.html][IMG]http://i1339.photobucket.com/albums/o711/Shrads_90/Capture1_zpsgszdjsk8.png[/IMG][/URL
])
And this is KAC defined as Protein in residuetypes.dat file:
[URL=
http://s1339.photobucket.com/user/Shrads_90/media/Capture2_zpsye0jwtjd.png.html][IMG]http://i1339.photobucket.com/albums/o711/Shrads_90/Capture2_zpsye0jwtjd.png[/IMG][/URL
]
Please help me in knowing where I am going wrong.
Thanks in advance,
Shraddha
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