Dear Amber users,
I am trying to calculate pKa shift of a histidine residue in protein
using AMBER 11.
Therefore, I need to perform alchemical shift from HIP to HIE.
For that, I followed the tutorial below,
http://ambermd.org/tutorials/advanced/tutorial9/
and it went well until the step 1 where charge is removed.
However, I got a problem in step 2 where the atom is supposed to disappear.
My calculation seems to be running, but it doesn't produce anything.
The two output files stay like below for more than half an hour and
produce nothing.
process 0 (This is the end of the file)
| MPI Timing options:
| profile_mpi = 0
Zero-Charge Mask .16; matches 1 atoms
Removing charge of 0.3866 from atom 16
Total charge of 0.3866 removed
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 400.000 ps
Number of triangulated 3-point waters found: 766
process 1
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
Here are also my two input files for process 0 and 1
process 0
&cntrl
imin=0, ntb=2, ntx=5, irest=1,
cut=8.0, ntp=1,
temp0=310.0, ntf=1, ntc=2,
ntt=3, gamma_ln=5.0,
nstlim=500000, dt=0.002, iwrap=1,
ntpr=500, ntave=500, ntwx=50000,
icfe=1, clambda=0.04691, ifsc=1, crgmask='.16', scmask='.16',
/
process 1
&cntrl
imin=0, ntb=2, ntx=5, irest=1,
cut=8.0, ntp=1,
temp0=310.0, ntf=1, ntc=2,
ntt=3, gamma_ln=5.0,
nstlim=500000, dt=0.002, iwrap=1,
ntpr=500, ntave=500,
icfe=1, clambda=0.04691,
/
This seems to be the problem of softcore potentials because there was no
error occurred in step 1.
I also searched the mailing list for the solution, and I found a similar
case, but there is no solution.
Is there anyone who can help me with this problem?
Cheers,
Wook
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Received on Thu Jul 19 2012 - 07:00:02 PDT
