Step 1: Generate Gromacs input files from a PDB structure

Beta Version (Why is this beta?)

Basically, follow standard PDB formatting. Here is a sample pdb file, so you can see the format expected by the webtool.
Your pdb file MUST conform to the following standards.

• No hidden characters. They can lead to unpredictable results. To avoid accidentally inserting them use a text editor such as vi, or emacs.
• If your file does not work with the page, only include lines that start with "ATOM" (to specify each atom), "TER" (to indicate a break between 2 chains) and "END" at the end of the file.
• Chain identifiers are not used. If you have multiple chains, insert "TER" (left justified) between chains. The webtool will internally index the chains sequentially, starting with 1.
• Terminal oxygens (in proteins) are called, OXT and O (not O1 and O2).
• The file is not read past an "END" statement (ALL CAPS, left justified). If atoms appear after an END line, these atoms will not be included.

Recognized residues include:

• Protein residues : All 20 amino acids (3 letter codes used).
• RNA residues: CYT or C, GUA or G, URA or U and ADE or A.
• DNA residues: DG, DC, DA, DT.
• Ligands: SAM (S-Adenosylemethionine), GNP (Gpp(NH)p), ATP, ADP, AMP

A contact map is a list of atom-atom pairs that are "in contact" in the native structure (the pdb structure). These pairs will interact via 6-12 interactions with the energetic minimum at the distance found in the pdb structure. There are three supported ways of defining a contact map.

• Shadow map (Recommended for Proteins) A shadow map includes contacts that are within a cutoff distance, are separated in sequence, and do not have an atom in between them. A full description can be found here. If you select this option, a shadow map will be generated and used in the Hamiltonian, with default values.
• Cut-off map (Recommended for RNA/DNA or mixed nucleic-amino acid systems) This will generate a list of contacts as determined by your specified distances and sequence differences. Recommended values are the defaults. This option is NOT enabled for CA model.
• Upload file Upload your own contact map. The contact file requires the following format: Each line identifies a single contact. Each line has 4 fields (chain i, atom number i , chain j, atom number j). For example, to include a contact between the atom 10 (pdb numbering) of the first chain (internally indexed as 1) and atom 20 of the third chain, the line would read:
  1 10 3 20
  Blank lines, even at the end of the file can cause trouble.

If you are using the CA model, then use residue numbers, not atom numbers.

There are currently 2 levels of graining available, All-Atom and C-alpha:

• All-Atom All non-hydrogen atoms will be included. If you have hydrogens in your pdb file, they SHOULD be ignored by this program. But, if you have given hydrogens non-standard names, then the program may complain. A complete description of the All-atom model can be found here for proteins and RNA/DNA. NOTE: the exact choice of parameters is up to you. The default values on this page are suggested values and are not necessarily identical to these references. Always double check your choice of parameters.
• C-alpha The C-alpha model is described in Clementi C, Nymeyer H & Onuchic JN (2000) J. Mol. Biol., 298, 937-953.

The default values are the values used in the initial protein and RNA papers, with the following modifications:

• The harmonic dihedral angle constant that maintains planarity of rings has been increased from 10 to 40. This makes the rings more rigid.

This is the ratio of the total stabilizing energy in ALL contacts and the total stabilizing energy in ALL flexible dihedrals (i.e. not ring, improper, or fixed dihedral angles). This quantity is fully described elsewhere. The sum of the strengths of all contacts and all dihedrals is then normalized to the number of atoms in the system.

In this model, all protein backbone dihedral angles are given identical energetic weighting. All protein side chain dihedrals are also given identical energetic weighting. This quantity sets the ratio of the strength of a single protein backbone dihedral to a single protein side chain dihedral.

In this model, all RNA/DNA backbone dihedral angles are given identical energetic weighting. All RNA/DNA side chain dihedrals are also given identical energetic weighting. This quantity sets the ratio of the strength of a single RNA/DNA side chain dihedral and a single RNA/DNA backbone dihedral.

One important feature of the model is the size of the atoms. These two parameters determine the excluded distance between non-native pairs and the strength of the repulsive term. We used 2.5 and 0.01 in our initial papers, but we leave these parameters flexible for additional investigation.

This software will recenter the system in a box with space between the system and the boundary. The box starts at the origin. This is useful when using periodic boundary conditions (which is required for grid neighbor searching in GROMACS). Make sure your box is large enough for the dynamics of interest. For example, if you are going to look at folding/unfolding, make sure you have a large buffer so that the molecule will not extend out of the box and interact with its own image. Pay particular attention to this settings if you are using a CA model, where the non-bonded cut-off distance is large.