I have attached flexible linker to a protein but found some unusual bonds (at attachment point 3-4 extra bonds found in attaching amino acid residue) at the point of attachment, I used coot for attachment. Gromacs can't read it properly and not being proceed further. Energy minimization wrote energy after 14 steps that I know insignificant (Potential energy is also positive). I might be sure that is because of improper attachment of linker and protein.
Could anyone please help me to refine the structure. or another things should I care about.
The only bonds that actually exist are the ones that are written in the topology, not what might be visualized in various software. You'll have to provide better detail of how you prepared the residue definition(s), because all this boils down to is adding a custom residue.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Hi I suggest to edit the file in another environment such as schrodinger maestro. After your modifications you can perform protein preparation wizard and a minimization by using macromodel. After that you can export the file as pdb and probably gromacs can read the file easier (since I have seen that the modified residue are aminoacids). In this way I suppose that gromacs can correctly recognize the strucutre during its preparation.
Sincerely
Simone
Easy answer: use a modelling program like WHAT IF or it's close relative YASARA (the latter has better graphics, interface to MD etc.). Look for them on the web.
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