joao@trial_joao: gmx pdb2gmx -f protein.pdb -o protein.gro -ter -ignh
GROMACS:    gmx pdb2gmx, VERSION 5.0.4

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Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
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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:
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GROMACS:      gmx pdb2gmx, VERSION 5.0.4
Executable:   /home/software/science/gromacs5/bin/gmx
Library dir:  /home/software/science/gromacs5/share/gromacs/top
Command line:
  gmx pdb2gmx -f protein.pdb -o protein.gro -ter -ignh


Select the Force Field:
From '/home/software/science/gromacs5/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: CHARMM36 all-atom force field (April 2015)
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 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
9

Using the Charmm36-apr2015 force field in directory charmm36-apr2015.ff

Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/watermodels.dat

Select the Water Model:
 1: TIP3P   TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
 2: TIP4P   TIP 4-point
 3: TIP5P   TIP 5-point
 4: SPC     simple point charge
 5: SPC/E   extended simple point charge
 6: None
1
Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/merged.r2b
Reading protein.pdb...
Read 123 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 15 residues with 123 atoms

  chain  #res #atoms
  1 ' '    15    123

All occupancies are one
Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/atomtypes.atp
Atomtype 384
Reading residue database... (charmm36-apr2015)
Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/merged.rtp
Residue 699
Sorting it all out...
Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/merged.hdb
Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/merged.n.tdb
Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/merged.c.tdb
Processing chain 1 (123 atoms, 15 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 28 donors and 22 acceptors were found.
There are 41 hydrogen bonds
Will use HISE for residue 28
Identified residue GLY22 as a starting terminus.
Identified residue GLU36 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                   HIS28
                   NE253
   MET32    SD86   0.693
Select start terminus type for GLY-22
 0: GLY-NH3+
 1: GLY-NH2
 2: 5TER
 3: None
1
Start terminus GLY-22: GLY-NH2
Select end terminus type for GLU-36
 0: COO-
 1: COOH
 2: CT2
 3: 3TER
 4: None
1
End terminus GLU-36: COOH
Opening force field file /home/software/science/gromacs5/share/gromacs/top/charmm36-apr2015.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 15 residues with 255 atoms
Making bonds...
Number of bonds was 256, now 256
Generating angles, dihedrals and pairs...
Before cleaning: 661 pairs
Before cleaning: 666 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   13 cmap torsion pairs
There are  666 dihedrals,   43 impropers,  460 angles
           658 pairs,      256 bonds and     0 virtual sites
Total mass 1781.090 a.m.u.
Total charge 3.000 e
Writing topology

Writing coordinate file...
		--------- PLEASE NOTE ------------
You have successfully generated a topology from: protein.pdb.
The Charmm36-apr2015 force field and the tip3p water model are used.
		--------- ETON ESAELP ------------

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