Dear All,
I'm getting positive Amber FF energy values after I stripped the solvent,
and ions.
I did this for other proteins recently and got meaningful and -ve E values.
Thus I'm a bit puzzled about what these energy values might mean.
Visual inspection of the structure did not reveal anything strange and the
structure looks fine.
Thus can you please comment as to what might be wrong here and how can I
possibly fix this problem?
Sample Es for stripped protein
NSTEP ENERGY RMS GMAX NAME NUMBER
1 * 7.7864E+02 1.9139E+01* 1.1727E+02 FE 1491
BOND = 284.3194 ANGLE = 828.9885 DIHED =
508.5032
VDWAALS = -682.0879 EEL = -4975.7223 HBOND =
0.0000
1-4 VDW = 343.3292 1-4 EEL = 4397.5842 RESTRAINT =
0.0000
CMAP = 73.7232
minimization completed, ENE= 0.77863756E+03 RMS= 0.191394E+02
TRAJENE: Trajectory file ended
TRAJENE: Trajene complete.
Sample E for solvated protein
NSTEP ENERGY RMS GMAX NAME NUMBER
1 * -6.1452E+04 1.3795E+01* 1.3013E+02 C 727
BOND = 308.1534 ANGLE = 820.6275 DIHED =
504.6346
VDWAALS = 8617.0697 EEL = -75800.8695 HBOND =
0.0000
1-4 VDW = 337.3554 1-4 EEL = 3694.9279 RESTRAINT =
0.0000
CMAP = 66.4508
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Wed Dec 16 2020 - 09:00:02 PST
