[gmx-users] Acetylation of lysine

[Shraddha Parate]

Using the Gromos45a3 force field in directory ./gromos45a3.ff

Opening force field file ./gromos45a3.ff/aminoacids.r2b
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 pro
per 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.33#
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.
Warning: Residue KAC31 in chain has different type (Other) from starting
residue GLY1 (Protein).
Warning: Residue KAC32 in chain has different type (Other) from starting
residue GLY1 (Protein).
Warning: Residue KAC33 in chain has different type (Other) from starting
residue GLY1 (Protein).
Warning: Residue HIS34 in chain has different type (Protein) from starting
residue GLY1 (Protein).
Warning: Residue PRO35 in chain has different type (Protein) from starting
residue GLY1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.

Identified residue HIS30 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 HIS-30: 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
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