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 = **********
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.
----Hyma
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: min.out
- application/octet-stream attachment: heat.out
Received on Thu Feb 25 2010 - 02:00:23 PST
