On Tue, 2015-04-14 at 17:12 +0530, Swithin Hanosh wrote:
> Dear Amber Users,
>
>
> I am trying to minimize a structure using sander. The minimization stops
> halfway between and returns the error "The system has extended beyond the
> extent of the virtual box". Please suggest the possible cause of error. The
> output file is attached with the mail.
I see this in your input file:
Minimize
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 0,
igb = 0,
cut = 12
/
This indicates that you are using a non-periodic potential with only a
12-angstrom cutoff. Later, I see this:
NATOM = 177635 NTYPES = 16 NBONH = 175116 MBONA = 2561
NTHETH = 5663 MTHETA = 3460 NPHIH = 11111 MPHIA = 8541
NHPARM = 0 NPARM = 0 NNB = 257752 NRES = 57861
NBONA = 2561 NTHETA = 3460 NPHIA = 8541 NUMBND = 62
NUMANG = 124 NPTRA = 57 NATYP = 42 NPHB = 1
IFBOX = 2 NMXRS = 49 IFCAP = 0 NEXTRA = 0
NCOPY = 0
...
Number of triangulated 3-point waters found: 57541
This tells me that your system is clearly an explicitly solvated system
with defined periodic boundaries. While this may not be your problem,
your input file *should* be setting ntb=1. I also suggest using a
shorter cutoff (something between 8 and 10 A). For non-periodic
simulations, you should use a much larger cutoff.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 14 2015 - 07:30:04 PDT
