maiia@SpectrumAnalayzer:~/Рабочий стол/Protein$ gmx pdb2gmx -f 2OOB.pdb -o peptide.pdb -ff amber99sbmut -water tip3p -ignh
                  :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

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 Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner
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   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers
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                           and the project leaders:
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GROMACS:      gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx pdb2gmx -f 2OOB.pdb -o peptide.pdb -ff amber99sbmut -water tip3p -ignh


Using the Amber99sbmut force field in directory /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff

Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.r2b
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/dna.r2b
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/rna.r2b
Reading 2OOB.pdb...
Read 1056 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Moved all the water blocks to the end
There are 2 chains and 2 blocks of water and 248 residues with 1056 atoms

  chain  #res #atoms
  1 'A'    44    350
  2 'B'    72    574
  3 ' '    50     50  (only water)
  4 ' '    82     82  (only water)


WARNING: there were 0 atoms with zero occupancy and 2 atoms with
         occupancy unequal to one (out of 1056 atoms). Check your pdb file.

Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/atomtypes.atp
Atomtype 103
Reading residue database... (amber99sbmut)
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.rtp
Residue 98
Sorting it all out...
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/dna.rtp
Residue 114
Sorting it all out...
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/mutres.rtp
Residue 666
Sorting it all out...
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/rna.rtp
Residue 682
Sorting it all out...
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.hdb
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/dna.hdb
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/rna.hdb
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.n.tdb
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.c.tdb
Processing chain 1 'A' (350 atoms, 44 residues)
Identified residue LEU1 as a starting terminus.
Identified residue PHE44 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/dna.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 44 residues with 707 atoms
Chain time...
Making bonds...
Number of bonds was 711, now 710
Generating angles, dihedrals and pairs...
Before cleaning: 1858 pairs
Before cleaning: 1858 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 1858 dihedrals,  139 impropers, 1284 angles
          1846 pairs,      710 bonds and     0 virtual sites
Total mass 4981.738 a.m.u.
Total charge -2.000 e
Writing topology
Processing chain 2 'B' (574 atoms, 72 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 109 donors and 113 acceptors were found.
There are 165 hydrogen bonds
Will use HISE for residue 68
Identified residue MET1 as a starting terminus.
Identified residue ARG72 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    MET1
                     SD7
   HIS68  NE2540   1.673
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/dna.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 72 residues with 1174 atoms
Chain time...
Making bonds...
Number of bonds was 1181, now 1180
Generating angles, dihedrals and pairs...
Before cleaning: 3128 pairs
Before cleaning: 3148 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 3148 dihedrals,  204 impropers, 2155 angles
          3119 pairs,     1180 bonds and     0 virtual sites
Total mass 8180.452 a.m.u.
Total charge -1.000 e
Writing topology
Processing chain 3 (50 atoms, 50 residues)
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/dna.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 50 residues with 150 atoms
Making bonds...
Number of bonds was 100, now 100
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are    0 dihedrals,    0 impropers,   50 angles
             0 pairs,      100 bonds and     0 virtual sites
Total mass 900.800 a.m.u.
Total charge 0.000 e
Processing chain 4 (82 atoms, 82 residues)
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/aminoacids.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/dna.arn
Opening force field file /home/maiia/.local/lib/python2.7/site-packages/pmx/data/mutff45/amber99sbmut.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 82 residues with 246 atoms
Making bonds...
Number of bonds was 164, now 164
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are    0 dihedrals,    0 impropers,   82 angles
             0 pairs,      164 bonds and     0 virtual sites
Total mass 1477.312 a.m.u.
Total charge 0.000 e
Including chain 1 in system: 707 atoms 44 residues
Including chain 2 in system: 1174 atoms 72 residues
Including chain 3 in system: 150 atoms 50 residues
Including chain 4 in system: 246 atoms 82 residues
Now there are 2277 atoms and 248 residues
Total mass in system 15540.302 a.m.u.
Total charge in system -3.000 e

Writing coordinate file...
        --------- PLEASE NOTE ------------
You have successfully generated a topology from: 2OOB.pdb.
The Amber99sbmut force field and the tip3p water model are used.
        --------- ETON ESAELP ------------

gcq#498: "Problems worthy of attack prove their worth by hitting back." (Piet Hein)