[gmx-users] Adding new residues and pdb2gmx

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 15 08:02:27 CET 2012

On 15/02/2012 5:00 PM, Jernej Zidar wrote:
> Hi.
>    I've downloaded the charmm36 (gromacs-charmm36.ff_4.5.4.tgz) and
> added some residues to it by editing the lipids.rtp file. I also plan
> to use pdb2gmx to convert CHARMM-generated PDB files to GRO format.
> The Gromacs manual suggests one should create a residuetypes.dat file
> in the parent directory containing all the residues present in the RTP
> files.
>    After doing so I used CHARMM (using CHARMM36 lipid forcefield) to
> generate the PDB of the lipid LPPC and run: pdb2gmx -f lppc.pdb -water
> none -noter -ff charmm36 -v.
>    pdb2gmx appears to hang (100 % usage of one computer core) at the
> last line of the following messages:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>    -f       lppc.pdb  Input        Structure file: gro g96 pdb tpr etc.
>    -o       conf.gro  Output       Structure file: gro g96 pdb etc.
>    -p      topol.top  Output       Topology file
>    -i      posre.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 charmm36  Force field, interactive by default. Use -h for
>                              information.
> -water       enum   none    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   no      Interactive termini selection, iso charged
> -[no]lys     bool   no      Interactive lysine selection, iso charged
> -[no]arg     bool   no      Interactive arginine 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 coordinate
>                              file
> -[no]missing bool   no      Continue when atoms are missing, dangerous
> -[no]v       bool   yes     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
> Using the Charmm36 force field in directory ./charmm36.ff
> Opening force field file ./charmm36.ff/aminoacids.r2b
> Opening force field file ./charmm36.ff/rna.r2b
> Reading lppc.pdb...
> Read 70 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 70 atoms
>    chain  #res #atoms
>    1 ' '     1     70
> All occupancies are one
> Opening force field file ./charmm36.ff/atomtypes.atp
> Atomtype 1 (after that I abort the command with CTRL+C)
> - - -
>    The LPPC residue is present in both the ./residuetypes.dat and
> ./charmm36/lipids.rtp files. What's wrong? I would really like to
> increase the verbosity of the pdb2gmx command but it seems the "-v"
> switch has no/little effect.

The most likely explanation is that you've not followed a file format 
somehow. A blank line at the end of a file you've modified might be 
required. If you've edited using some broken editor, dos2unix might be 
your friend.

Check the original charmm36 forcefield works on some simple protein 
case. Then check that case works with your modified forcefield.


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