Dear all,
I have 2 separate PDB files (2 monomers of the same dimer) and I want to put them in one PDB file (PDB file of my final dimer).
I opened the 2 monomers on PYMOL, did a select all and saved the complex but I think that PYMOL have generated some unwanted CONNECT!! (at a first glance, I have more CONNECT for one chain than what I had in the original PDB file?!!!
Any explication? I can't verify all the CONNECT so how can I make sure that my final PDB is good (I need it to be perfect because I will use it as input in GROMACS).
Thank you in advance for your help.
You can use YASARA or Discovery studio its easy and if your looking for dimers there is an option to make dimer from monomer ,check pymol tut
VMD has a script to merge pdbs: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mergepdbs/
Chimera supports a command to merge pdbs: http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006245.html
Since PDBs are simple text files, you can in theory also simply merge them (cat file1.pdb file2.pdb > file3.pdb in linux or open them in text editor, select everything and copy to a new one). This may pose some problems, though, as the numbering of atoms / residues and CONECT lines won't be correct (which in many cases doesn't really matter). You can try copying only ATOM / HETATM lines. You can also open such lines in pymol and resave it, which may help.
Thank you for you answers.
Actually I though to erase the CONNECT lines but I hesitated specially because I will use this PDB file to run a molecular dynamic on GROMACS and I think that they are necessary specially when building the toplogy file. What do you think?
Use moleman ( http://xray.bmc.uu.se/markh/usf/) for all type pdb modification and correct the nomenclature.
Do energy minimization to remove unwanted clashes.
Pymol does not create CONNECT records, but draws bonds based on a distance criterium. Therefore if the exported structure file shows spurious bonds upon reloading, your monomers are clashing. Is your protein a dimer but appears as monomer in the pdb file? The monomers may be related by crystallographic symmetry. In this case, download the biological unit from the pdb and specify "set all_states, on" to get the correct dimer. To create a file with both monomer in state 1, first use "split_states to create separate objects of the two monomer, then use the "alter" command to change the chain label of one of the two monomers, then join the two monomers into a single object using "create".
If there is no structure of the dimer, you need a proper docking program/server to create the dimer with concommittant side chain rotamer optimization and energy minimization, otherwise clashes in your dimer model will make it fall apart during MD
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