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 GROMACS:    gmx pdb2gmx, VERSION 5.0.4 (double precision)

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

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

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GROMACS:      gmx pdb2gmx, VERSION 5.0.4 (double precision)
Executable:   /share/apps/gmx-double-multicore/bin/gmx_d
Library dir:  /share/apps/gmx-double-multicore/share/gromacs/top
Command line:
  gmx_d pdb2gmx -f proline.pdb -ter


Select the Force Field:
From '/share/apps/gmx-double-multicore/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: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file /share/apps/gmx-double-multicore/share/gromacs/top/oplsaa.ff/watermodels.dat

Select the Water Model:
 1: TIP4P  TIP 4-point, recommended
 2: TIP3P  TIP 3-point
 3: TIP5P  TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
 4: TIP5P  TIP 5-point improved for Ewald sums
 5: SPC    simple point charge
 6: SPC/E  extended simple point charge
 7: None
1
Opening force field file /share/apps/gmx-double-multicore/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading proline.pdb...
Read 8 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 1 residues with 8 atoms

  chain  #res #atoms
  1 'P'     1      8

All occupancies are one
Opening force field file /share/apps/gmx-double-multicore/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 815
Reading residue database... (oplsaa)
Opening force field file /share/apps/gmx-double-multicore/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 54
Sorting it all out...
Opening force field file /share/apps/gmx-double-multicore/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file /share/apps/gmx-double-multicore/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file /share/apps/gmx-double-multicore/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.4#
Processing chain 1 'P' (8 atoms, 1 residues)
Identified residue PRO1 as a starting terminus.
Identified residue PRO1 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for PRO-1
 0: PRO-NH2+
 1: PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one residue)
 2: PRO-NH
 3: NH3+
 4: ZWITTERION_NH3+ (only use with zwitterions containing exactly one residue)
 5: None
1
Start terminus PRO-1: PRO-ZWITTERION_NH2+
Select end terminus type for PRO-1
 0: PRO-COO-
 1: PRO-ZWITTERION_COO- (only use with zwitterions containing exactly one residue)
 2: COOH
 3: None
1
End terminus PRO-1: PRO-ZWITTERION_COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 17 atoms
Making bonds...
Number of bonds was 17, now 17
Generating angles, dihedrals and pairs...
Before cleaning: 46 pairs
Before cleaning: 51 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   51 dihedrals,    1 impropers,   33 angles
            46 pairs,       17 bonds and     0 virtual sites
Total mass 115.128 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.3#

Writing coordinate file...

Back Off! I just backed up conf.gro to ./#conf.gro.3#
		--------- PLEASE NOTE ------------
You have successfully generated a topology from: proline.pdb.
The Oplsaa force field and the tip4p water model are used.
		--------- ETON ESAELP ------------