Questions and problems?

Parm

My h-bonding energies are zero. I know that h-bonding is present... I got h-bonding using 4.0 - what is happening?

The new force field does not use hydrogen bonding terms.

In parm91.dat there were STDA parameters and STUB parameters. However, they were eliminated in parm94.dat.

            FATAL:  No nonbond parameter set found with name = STDA

The vdw parameters in the Cornell et al. force field are MOD4 (parm.in line 2, the NAMNB variable).

NOTE: it would be a mistake to use the parm94.dat parameters with residues defined in the Weiner et al. manner (those in db4.dat and any others created prior to Cornell et al.), since the atom types are different. See old and new type definitions.

Web Masters <webadmin@www.amber.ucsf.edu>

Last modified: Wed Apr 10 16:37:04 PDT 1996