Hi,
I am trying to do umbrella sampling for flipping a proline from cis to
trans in ribonucleaseA. I have already a 600ps explicit solvent
equilibrium dynamics of the wildtype (P93 CIS). I use ptraj and use the
trajout filename restart command to take the 600 ps snapshot and make it a
restart file. I think the first problem arises here. Because when I look
at the restart file, all the waters at the end have coordinates zero (I
have not specified for the waters to be excluded).
This is my input file:
minimization run
&cntrl
imin=0,irest=1,ntx=7,ntp=1,
nstlim=1000, ntt=1,
scee=1.2, ntpr=50, pencut=1,
vlimit=10,nmropt=0,
ntb=2,ntc=2,ntf=2,
maxcyc=500, ncyc=500,
ntwe=100, ntwx=100, ntpr=25,
&end
&wt type='REST' , istep1=0,value1=1, &end
&wt type='END' &end
LISTOUT=POUT
DISANG=RST.f
and this is my RST.f file:
# chirality for residue 1 atoms: CA C 0 CA+1
&rst iat= 1361, 1378, 1380, 1390, nstep1=1,
r1=0., r2=15., r3=25., r4=40., rk2 = 80., rk3=80., &end
When I run this on our redhat 9 linux cluster (with the nmropt=1), it
goes all the way to this stage:
RESTRAINTS:
Requested file redirections:
LISTOUT = POUT
DISANG = RST.f
Restraints will be read from file: RST.f
Here are comments from the DISANG input file:
# chirality for residue 1 atoms: CA C 0 CA+1
Number of restraints read = 1
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 5755
and then it hangs there.When I run it on Lemieux supercomputer in
Pittsburgh, it goes all the way to the same place and then it complains that
NMROPT is not zero and it can't reorder the waters. When I change NMROPT
to 0 and rerun it on Lemieux, it goes all the way to here:
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.1990E-14 at 2.461500
| CHECK d/dx switch(x): max rel err = 0.7670E-11 at 2.772760
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1000520
| TOTAL SIZE OF NONBOND LIST = 3977238
and then it crashes. The stdout and stder files don't give me anything
meaningful. Can someone help me out please?
Thanks
Mey
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Received on Wed Jan 14 2004 - 15:53:11 PST
