[gmx-users] Adding new residues and pdb2gmx
Mark.Abraham at anu.edu.au
Wed Feb 15 08:02:27 CET 2012
On 15/02/2012 5:00 PM, Jernej Zidar wrote:
> 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.
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
Check the original charmm36 forcefield works on some simple protein
case. Then check that case works with your modified forcefield.
More information about the gromacs.org_gmx-users