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Martinize and uncharged lysine side chain
- danijoo
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7 years 6 months ago #5873
by danijoo
Martinize and uncharged lysine side chain was created 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.
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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- jbarnoud
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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.
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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