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bond
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13 years 6 months ago #430
by yuhui234
bond was created by yuhui234
how to deal with S-S bridge bond between two cys residues in a protein structure , in cg simulation?
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- siewert
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13 years 5 months ago #431
by siewert
Replied by siewert on topic bond
The Cys-Cys bridge can be modeled as a standard type bond with d=0.39 nm and K=5000 kJ/(mol nm2). See Table 4 of the Martini Protein Forcefield paper.
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- yuhui234
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13 years 5 months ago #432
by yuhui234
Replied by yuhui234 on topic bond
how to deal with it? when a atomic structure became to a cg structure. it was generated by default set up? or it is require special script to deat with S-S bond?
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- xavier
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13 years 4 months ago #440
by xavier
Replied by xavier on topic bond
No! Cys-Cys bonds are not generated automatically. You have to insert them manually in the topology, in the bond section.
XAvier.
XAvier.
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13 years 4 months ago #442
by yuhui234
Replied by yuhui234 on topic bond
can you say it in detials? Thank you very much!
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13 years 4 months ago #445
by xavier
Replied by xavier on topic bond
The definition of bonds in the topology of a molecule is described in the GROMACS manual. I advise you to have a good look to understand how things are actually done ...
in short you have to add a line in the bond section of your topology and it would look like:
X Y 2 0.39 5000
where
X= index number of atom1,
Y= index number of atom2,
2= function type,
0.39= equilibration distance,
5000= force constant
in short you have to add a line in the bond section of your topology and it would look like:
X Y 2 0.39 5000
where
X= index number of atom1,
Y= index number of atom2,
2= function type,
0.39= equilibration distance,
5000= force constant
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