server).
<li>
Disulfide bonds are read from PDB based on SSBOND records and for multichain
-protein COMPND record with propers CHAIN: tokens listing all chains in the
-PDB file. See example:
+protein proper chain records are necessary. See example:
<pre>
-COMPND 3 CHAIN: A, B, C, D;
SSBOND 1 CYS C 107 CYS C 138
SSBOND 2 CYS C 124 CYS C 139
SSBOND 3 CYS C 137 CYS C 149
Distance distribution (from SAXS experiment) can be added for MREMD
simulation in advanced mode. First column distance in Angstroms, second column
distribution function value (separated by space).
+<li>
+Secondary structure restraints can be added to MD and MREMD
+simulation in advanced mode. Sequence of letters H,E and C or - for each
+residue is used to input helical, extended and no restraints, respectively.
</ol>
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