1. In bond_AM1.parm the last numeric column is the hydrodynamic radius of a side chain.
2. The last 20 numbers in scinter_LJ.parm are the "van der Waals radii" of the side chains; the types are ordered as in the Miyazawa-Jernigan table. You can also retrieve these numbers in the edited form if you run any system, specifying
setenv PRINT_PARM YES
in the unres.csh or other unres script file.
If you specify the usually used scinter_GB.parm, the output will contain the "side to side" cross-section dimensions of side chains and also anisotropies.
Re: Approximate amino acid size
Yes, in two types of files.
1. In bond_AM1.parm the last numeric column is the hydrodynamic radius of a side chain.
2. The last 20 numbers in scinter_LJ.parm are the "van der Waals radii" of the side chains; the types are ordered as in the Miyazawa-Jernigan table. You can also retrieve these numbers in the edited form if you run any system, specifying
setenv PRINT_PARM YES
in the unres.csh or other unres script file.
If you specify the usually used scinter_GB.parm, the output will contain the "side to side" cross-section dimensions of side chains and also anisotropies.
Adam
Re: Approximate amino acid size
Many Thanks, Adam.
Best,
Istvan