[gmx-users] Acetylation of lysine

Shraddha Parate parateshraddha at gmail.com
Wed Jan 24 03:01:06 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

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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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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:
[image: Inline image 1]

And this is KAC defined as Protein in residuetypes.dat file:

[image: Inline image 2]

Please help me in knowing where I am going wrong.

Thanks in advance,

Shraddha

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