[gmx-users] Adding new residues and pdb2gmx

Jernej Zidar jernej.zidar at gmail.com
Wed Feb 15 07:00:48 CET 2012

  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

  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
-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
-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
-[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.

Thanks in advance,
Jernej Zidar

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