Date: Sun Nov 16 2003 - 02:09:54 CST
I want to use NAMD program to do a MD calculation on an enzyme with two zinc
ions. I see CHARMM topology file has include zinc ion. However when I generate psf
and pdb file, there is only one zinc ion. How should I solve this problem?
As for a small ligand, though the NAMD tutorial said MOE and SPARTAN can
generate force field for novel system, I can't get MOE because it isn't free. As
to SPARTAN, I am not quite clear on how to genarate those parameters.I can only
find charge in the output file.
As we know, there are many parameters for a molecule such as bond,angle,dihedral
angle,etc, need I calculate them with Spartan ,then type them in topology and
parameter file in NAMD program? If yes, it is so complicated. Whether is there
software which can generate topology and parameter file for NAMD program?
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