Hi David,
I posted my response to the question that you asked and I deleted all the
unrelated posts while answering, it seems nobody saw that post.
So, here I am posting again:
I am performing the simulation of protein-ligand complex. The protein was
prepared using ff99SB forcefield and for the ligand I used GLYCAM_06
forcefield. I performed a restrained minimization first and then
unrestrained minimization [all minimization without SHAKE]. After that
heated the system slowly 0 to 300 K for 20ps and then density equilibration
and finally equilibration for 50ps. I was getting the SHAKE error:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 392 803 804
So, I looked at the structure as advised by David and found a close contact
between the water molecule's O and H atoms (803 and 804). I performed a
check of my structure using tleap's check command for the unrestrained
minimized structure and it was all okay. The problem arises during heating
step as I found some close contacts after checking the structure obtained
from heating step.
I repeated minimization, heating, density and equilibration steps with a
large solvated box (15, previously it was 21) and large cutoff for
calculation (12, previously it was 10). But the problem always arises after
the heating step. I even increased the heating time and results are still
the same. Could you please tell me where am I going wrong??
Regards
BM
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Received on Mon Jun 27 2016 - 18:00:02 PDT
