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Approximate amino acid size

Hi,

Is there any parameter in the PARAM directory that can be interpreted as the approximate size/volume of an amino acid side chain?

Thanks,

Istvan

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

Many Thanks, Adam.

Best,

Istvan