Cen Gao wrote: " Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow:"

Hi, the problem may be here the template sequence count and the pdb sequence count is not same.

In most pdb structures, we could find an amino acid missing at the begining.

Verify whether the first template sequence aa is same with first aa in pdb sequence(spdbv control panel).

probably you can get some other template of if theres no good alignment for that first amino acid, simply remove it.

May this work

regards, johnwin