Dear Amber users,
I know that the "vlimit exceeded for step" error is an over discussed
subject, but after I read almost everything I found in the list archive
about this, I still can not find an explanation to what is happening to
my system.
I am have 2 protein mutants differing on one amino acid each. I've
minimized the systems for both of them using the same input file and
everything went on smoothly. When I heat the system however one of the
systems is behaving very strangely, in the way that after my first step
I get the following errors:
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> = 0.0
> Etot = -119235.7327 EKtot = 0.0000 EPtot =
> -119235.7327
> BOND = 120.1323 ANGLE = 762.7237 DIHED =
> 3442.2867
> 1-4 NB = 1372.0187 1-4 EEL = 15491.2504 VDWAALS =
> 4621.6183
> EELEC = -145045.7628 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> Ewald error estimate: 0.4162E-03
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> vlimit exceeded for step 2; vmax = 33.0050
> vlimit exceeded for step 3; vmax = 25.9657
The other mutant is behaving perfectly normal. The first heating step of
the normal systems is:
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> = 0.0
> Etot = -118584.5154 EKtot = 0.0000 EPtot =
> -118584.5154
> BOND = 173.2443 ANGLE = 649.6741 DIHED =
> 3460.2710
> 1-4 NB = 1440.2548 1-4 EEL = 15643.6343 VDWAALS =
> 5594.6009
> EELEC = -145546.1948 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> Ewald error estimate: 0.4910E-03
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
I do not see any major differences however, one is running and one is not.
The input file that I use is:
> heat 1modnew pdb model
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=25000,dt=0.002,
> ntc=2,ntf=2,
> cut=11.0, ntb=1,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> ntr=1,
> restraint_wt=2.0,
> nmropt=1,
> restraintmask = '(:1-359)',
> /
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
I checked the system after the minimization step and it looked fine. I
am running out of ideas, so any suggestion will be highly valued.
Thanks,
Cristina
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 21 2010 - 10:30:03 PDT
