Hello,
On Thu, Feb 25, 2010 at 4:54 AM, Hyma vathi <hymavathi.niper.gmail.com> wrote:
> Dear Amber Users,
>
> I am trying to perform MM-PBSA on a protein which is having a cofactor and a
> ligand. I have prepared the prepin and frcmod files for both the ligand and
> the cofactor and saved the prmtop and inpcrd files for the complex.I
> performed the first two stages i.e.,minimisation and heating. For
> minimisation I have given the following files:
> min.in:
> minimise 3bcj
> &cntrl
> imin=1,maxcyc=1000,ncyc=500,
> cut=8.0,ntb=1,
> ntc=1,
> ntpr=100,
> ntr=1, restraintmask=':1-317',
> restraint_wt=2.0
> /
> heat.in:
> heat 3bcj
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=25000,dt=0.002,
> ntc=1,
> cut=8.0, ntb=1,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> ntr=1, restraintmask=':1-317',
> restraint_wt=2.0,
> nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
>
> But the heat.out file has the following message:
>
> vlimit exceeded for step 48; vmax = **********
This is usually indicative of a poor contact (i.e. a couple atoms are
overlapping). It would probably be helpful to visualize the system
before and after the minimization restart file. Check that the system
was built the way you were expecting and that there are no bad
contacts. It may also be helpful to write out every frame to an mdcrd
file and run it for 5 steps to see why the system may be blowing
apart.
> vlimit exceeded for step 49; vmax = 763.0963
> vlimit exceeded for step 50; vmax = 1040.8560
> vlimit exceeded for step 51; vmax = **********
> vlimit exceeded for step 52; vmax = **********
> vlimit exceeded for step 53; vmax = 29291.9197
> vlimit exceeded for step 54; vmax = **********
> vlimit exceeded for step 55; vmax = **********
> vlimit exceeded for step 56; vmax = **********
> vlimit exceeded for step 57; vmax = **********
> .......................
> ..........................
> vlimit exceeded for step 2123; vmax = **********
> vlimit exceeded for step 2124; vmax = **********
> vlimit exceeded for step 2125; vmax = **********
> vlimit exceeded for step 2126; vmax = **********
> vlimit exceeded for step 2127; vmax = **********
>
> Can anyone help me where the problem is. I am attaching the min.out and
> heat.out files.
>
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Feb 25 2010 - 08:30:06 PST
