Dear CHAMBER developer:
I want to run CHARMM FF in AMBER. My workflow is:
1. created psf and pdb in CHARMM
2. use CHAMBER to generate prmtop and inpcrd
3. run one step energy calculation in CHARMM and sander, compare energy,
cutoff in both CHARMM and AMBER set to 999
Result:
All energy terms in CHARMM FF c22 are the same. All energy terms except
Dihedral are the same in c36. Dihedral energy is slightly off in c36 no
matter turning on or off CMAP. I tested on several proteins and here is the
result of DHFR in vacumm in c36:
#AMBER
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 300.85 PRESS =
0.0
Etot = 377.0066 EKtot = 2230.2661 EPtot =
-1853.2594
BOND = 149.5654 ANGLE = 463.7249 DIHED =
1517.7891
UB = 23.8425 IMP = 18.5436 CMAP =
68.8362
1-4 NB = 391.8176 1-4 EEL = 6625.6748 VDWAALS =
-1031.4918
EELEC = -10081.5617 EHBOND = 0.0000 RESTRAINT =
0.0000
#CHARMM
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals
IMPRopers
ENER CROSS: CMAPs PMF1D PMF2D PRIMO
ENER EXTERN: VDWaals ELEC HBONds ASP
USER
---------- --------- --------- --------- ---------
---------
ENER> 0 -1853.91175 0.00000 2.12417
ENER INTERN> 149.56538 463.72494 23.84247 1517.13684
18.54358
ENER CROSS> 68.83613 0.00000 0.00000 0.00000
ENER EXTERN> -639.67419 -3455.88690 0.00000 0.00000
0.00000
Can anybody give me some hint or point out where I did wrong?
Thanks!
Jun Feng
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Received on Fri Aug 30 2013 - 14:30:02 PDT
