[gmx-users] pdb2gmx stop at "AtomType 1"

Justin A. Lemkul jalemkul at vt.edu
Sat Oct 16 14:36:00 CEST 2010



Ó¢ÐÛ²»ÔÙ¼Åį wrote:
> Dear gmx-users,
>   I have added the required residue groups in the rtp file. Then I run 
> the pdb2gmx using the following line for the top file, only to stop at " 
> AtomType 1". No any message is given. I can not think out what is 
> happening at all. Please help me with this problem, thanks a lot. Note 
> that I am using gmx-4.5.

Did you also add an entry in residuetypes.dat and aminoacids.hdb (if necessary)?

-Justin

>   Chaofu Wu, Dr.
>  
> xiaowu759 at linux-s38y:~/workshop 
> <mailto:xiaowu759 at linux-s38y:~/workshop>> pdb2gmx -f deta.pdb -o 
> deta.gro -p deta.top -i deta.itp -ter
>                          :-)  G  R  O  M  A  C  S  (-:
>                Gromacs Runs One Microsecond At Cannonball Speeds
>                             :-)  VERSION 4.5.1  (-:
>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>         Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
>           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
>                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
>                Berk Hess, David van der Spoel, and Erik Lindahl.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>             Copyright (c) 2001-2010, The GROMACS development team at
>         Uppsala University & The Royal Institute of Technology, Sweden.
>             check out http://www.gromacs.org for more information.
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
>                                :-)  pdb2gmx  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f       deta.pdb  Input        Structure file: gro g96 pdb tpr etc.
>   -o       deta.gro  Output       Structure file: gro g96 pdb etc.
>   -p       deta.top  Output       Topology file
>   -i       deta.itp  Output       Include file for topology
>   -n      clean.ndx  Output, Opt. Index file
>   -q      clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -chainsep    enum   id_or_ter  Condition in PDB files when a new chain and
>                             molecule_type should be started: id_or_ter,
>                             id_and_ter, ter, id or interactive
> -ff          string select  Force field, interactive by default. Use -h for
>                             information.
> -water       enum   select  Water model to use: select, none, spc, spce,
>                             tip3p, tip4p or tip5p
> -[no]inter   bool   no      Set the next 8 options to interactive
> -[no]ss      bool   no      Interactive SS bridge selection
> -[no]ter     bool   yes     Interactive termini selection, iso charged
> -[no]lys     bool   no      Interactive Lysine selection, iso charged
> -[no]arg     bool   no      Interactive Arganine selection, iso charged
> -[no]asp     bool   no      Interactive Aspartic Acid selection, iso charged
> -[no]glu     bool   no      Interactive Glutamic Acid selection, iso charged
> -[no]gln     bool   no      Interactive Glutamine selection, iso neutral
> -[no]his     bool   no      Interactive Histidine selection, iso checking
>                             H-bonds
> -angle       real   135     Minimum hydrogen-donor-acceptor angle for a
>                             H-bond (degrees)
> -dist        real   0.3     Maximum donor-acceptor distance for a H-bond 
> (nm)
> -[no]una     bool   no      Select aromatic rings with united CH atoms on
>                             Phenylalanine, Tryptophane and Tyrosine
> -[no]ignh    bool   no      Ignore hydrogen atoms that are in the pdb file
> -[no]missing bool   no      Continue when atoms are missing, dangerous
> -[no]v       bool   no      Be slightly more verbose in messages
> -posrefc     real   1000    Force constant for position restraints
> -vsite       enum   none    Convert atoms to virtual sites: none, hydrogens
>                             or aromatics
> -[no]heavyh  bool   no      Make hydrogen atoms heavy
> -[no]deuterate bool no      Change the mass of hydrogens to 2 amu
> -[no]chargegrp bool yes     Use charge groups in the rtp file
> -[no]cmap    bool   yes     Use cmap torsions (if enabled in the rtp file)
> -[no]renum   bool   no      Renumber the residues consecutively in the 
> output
> -[no]rtpres  bool   no      Use rtp entry names as residue names
> 
> Select the Force Field:
>  From current directory:
>  1: CNT_OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>  2: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>  From '/usr/local/gromacs/share/gromacs/top':
>  3: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>  4: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>  5: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
>  6: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
>  7: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
>  8: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 
> 1950-58, 2010)
>  9: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 10: CHARMM27 all-atom force field (with CMAP) - version 2.0beta
> 11: GROMOS96 43a1 force field
> 12: GROMOS96 43a2 force field (improved alkane dihedrals)
> 13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 17: [DEPRECATED] Encad all-atom force field, using full solvent charges
> 18: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum 
> charges
> 19: [DEPRECATED] Gromacs force field (see manual)
> 20: [DEPRECATED] Gromacs force field with hydrogens for NMR
> 16
> Using the Oplsaa force field in directory oplsaa.ff
> Opening force field file oplsaa.ff/watermodels.dat
> Select the Water Model:
>  1: TIP4P  TIP 4-point, recommended
>  2: TIP3P  TIP 3-point
>  3: TIP5P  TIP 5-point
>  4: SPC    simple point charge
>  5: SPC/E  extended simple point charge
>  6: None
> 6
> Opening force field file oplsaa.ff/aminoacids.r2b
> Reading deta.pdb...
> Read 20 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> There are 1 chains and 0 blocks of water and 1 residues with 20 atoms
>   chain  #res #atoms
>   1 ' '     1     20 
> All occupancies are one
> Opening force field file oplsaa.ff/atomtypes.atp
> Atomtype 1
>  
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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