> I have done 2 calculatios, one of them using NAMD/amber force field, and the
> other one using NAMD/charmm force field. With the first one, no problem,
> everything goes OK, however, in the second case, I have problems. This is what
> I did:
>
> 1) With ptraj, I convert the NAMD trajectory in .dcd format to amber crd
> format
Make sure that "nobox" is specified on the trajout. Also, make sure there
is a 1-1 mapping between the coordinates in both; the easiest way to do
this is to take 1 snapshot from your .dcd file and re-build an AMBER
topology with this snapshot as a PDB.
trajin namd.dcd 1 1 1
trajout snap.pdb pdb
then run LEaP with this PDB to generate a new topology...
> BOND = 118264.5368 ANGLE = 19804.6937 DIHED = 1827.4664
> VDWAALS = 64582.4134 EEL = -10701.6010 EGB = -4928.3276
> 1-4 VDW = 141690.8806 1-4 EEL = 8520.1304 RESTRAINT = 0.0000
The large energies for the BAD (bond-angle-dihedral), but not
electrostatics, suggest the order may not be consistent. I would not
expect "charmm" geometries to lead to differences this large, but then
again I haven't tested this; most likely it is a different mapping
-- tec3
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Mar 16 2008 - 06:07:25 PDT
