AMBER Archive (2008)

Subject: Re: AMBER: implicit energy calculations

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Thu Mar 13 2008 - 12:47:04 CDT

> 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
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