hi i'm new to gromacs and am trying to construct an initial configuration for a system of polymer chains. i've looked through previous posts to the mailing list (such as the one attached below) and read chapter 5 of the gromacs manual and the wiki, but it is still not clear to me how to construct the .pdb file of the polymer chain to be used as input for pdb2gmx to produce the .top file of the chain.
all of the gromacs examples i've found for .pdb files of proteins have the polypeptides defined atomistically, rather than in terms of monomers (amino acids). but i presume that defining the monomer topology in the .rtp and .tdb files should allow the topology of the polymer to be defined in terms of monomer units or at least in terms of the coordinates of the backbone atoms. is this correct? does anyone have an example of a .pdb file of a polymer that is defined in terms monomer units rather than atoms? thanks david >> Hi, >> >> I am trying to generate a polymer layer with 30 chains of 20 monomeric >> units using gromacs' genbox command. For that, I need to have .itp file >> for the single polymer chain (polystyrene). I have .itp file for styrene >> molecule, how can I make a .itp file for polymer chain using .itp file >> of styrene? I guess there must be some way to use parameters of styrene >> molecule to build up a .itp file for the polymer. >> I would appreciate If someone can help me with this. > For a given n, you can build an n-styrene .top file with pdb2gmx. For > this to work, you need a styrene .rtp file entry that defines head and > tail atoms in a manner analogous to the peptide .rtp file entries, and > probably you will also need to make .tdb entries to cap the chains. Read > the relevant sections of chapter 5 and the wiki thoroughly, and > experiment with this mechanism on peptides (where it already works) > before trying to build the elements for your system. > Once you have the .rtp and .tdb entries constructed, you give pdb2gmx a > structure file containing the 20-styrene molecule, and it uses the > residue numbering in that to infer the topology based on the .rtp entry. > Then you edit the .top file by hand to become a 20-styrene .itp file. > Then you can construct your 30-chain coordinate file somehow, #include > the 20-styrene .itp file, construct a .top file by hand, and make sure > its [ molecules ] entry has 30 styrene molecules. pdb2gmx might also be > able to handle the 30 20-styrene coordinate file directly with the right > command-line option, but I've never done it, so you're on your own there. > Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
