normal Martinize and uncharged lysine side chain

  • danijoo
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7 years 6 months ago #5873 by danijoo
Hello,

Im new to gromacs and martini and currently try to create a coarse grain model of a membrane protein which bears an uncharged Lysine residue in the sequence. From my testings and the source of martinize.py the script seems to add a charged lysine residues no matter whats in the pdb.

Is it correct that all I need to do is edit the .itp file and replace the Qd bead with a P1 and set the charge value to 1? The mapping scheme for Qd and P1 seems to be identical for both charged and uncharged lysine side chain.

Best regards,
Daniel B.

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7 years 2 months ago #6969 by jbarnoud
Replied by jbarnoud on topic Martinize and uncharged lysine side chain
Hi,

What you suggest seems sensible. You may have made a typo , though: you want to set the charge to 0, not 1.

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