AMBER: implicit energy calculations

From: <>
Date: Thu, 13 Mar 2008 17:26:43 +0100

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:


The output of this calculation gives no error, but very high values of the
energetic terms, for example:

minimizing coord set # 1

      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
1-4 VDW = 141690.8806 1-4 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

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Received on Sun Mar 16 2008 - 06:07:24 PDT
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