Dear all,
I am preparing a RNA system for MD simulation. The system consists of 2
modified RNA residues which are defined by Aduri et al.
The protocol consists of 1. prior minimization 2.Equilibration 3.
Minimization 4. Production MD
I am getting a problem after the 1st minimization step when i try to go for
equilibration commands. The job get abnormally terminated. Also, i checked
the output PDB of the rst file which shows distorted residues.
The mdout file shows something like this:
* NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
-6863.0 Etot = -85749.1605 EKtot = 0.0000 EPtot =
-85749.1605 BOND = 41.7370 ANGLE = 283.5417 DIHED
= 717.1987 1-4 NB = 316.9032 1-4 EEL = -2462.2275
VDWAALS = 11458.8455 EELEC = -96105.1590 EHBOND =
0.0000 RESTRAINT = 0.0000 EKCMT = 0.0000 VIRIAL =
34271.8077 VOLUME =
231284.2068 Density
= 0.8729 Ewald error estimate:
0.1272E-03 ------------------------------------------------------------------------------Coordinate
resetting (SHAKE) cannot be accomplished,deviation is too largeNITER, NIT,
LL, I and J are : 0 2 38 117 118 Note: This is
usually a symptom of some deeper problem with the energetics of the
system.*
When i had a look into the rst file of the previous minimization run, i
found that it cannot be opened or read.
I have tried using the system on both versions of AMBER (10 and 16). The
same error persists.
I am not getting a clue into how this can happen??
Thanks in advance......
Mr. Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
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Received on Sun Oct 16 2016 - 02:30:02 PDT
