AMBER Archive (2008)Subject: AMBER: implicit energy calculations
From: rebeca_at_mmb.pcb.ub.es
Date: Thu Mar 13 2008  11:26:43 CDT
Hello,
I am trying to do implicit solvent energy calculation (using sander) for a
trajectory of a protein I have previously generated with NAMD.
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
2) Using the generated .crd trajectory and the topology obtained with xleap, I
did the energy calculation using this input:
&cntrl
ntp=0,
maxcyc=1,
ntwx=1,
ntr=0,
ntb=0,
imin=5,
cut=99,
igb=1,
/
The output of this calculation gives no error, but very high values of the
energetic terms, for example:
POSTPROCESSING OF TRAJECTORY ENERGIES
minimizing coord set # 1
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.3906E+05 7.7217E+03 2.5847E+05 C 2571
BOND = 118264.5368 ANGLE = 19804.6937 DIHED = 1827.4664
VDWAALS = 64582.4134 EEL = 10701.6010 EGB = 4928.3276
14 VDW = 141690.8806 14 EEL = 8520.1304 RESTRAINT = 0.0000
....................
RMS is extremely high and gmax idem. Anybody knows how could I solve the
problem? I suppose it has to do with the difference in the parameters of the
atoms that the NAMD/charmm and sander calculation are using, but I am
not sure.
Any ideas will be very appreciated. Thanks a lot in advance.
Rebeca García Fandiño Ph. D.
Parc Cientific de Barcelona
Barcelona Spain
rebeca_at_mmb.pcb.ub.es

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