Hello everyone.
I try to run an implicit solvent simulation of protein with ligands. I've followed this tutorial (
https://ambermd.org/tutorials/basic/tutorial15/index.php) to set up the equilibration part of the simulation, so all input files are from there. The heating finishes without any error, but I cannot watch the system after this step by using vmd and .rst7 or .nc. So, I conclude that the output of the heating was corrupted.
The next equilibration step fails with the reading of heat.rst7 file with error:
|
|--------------------------------------------------------
| ERROR: I could not understand line 3
************************************************************************
*s in the inpcrd file often indicate an overflow of the Fortran format used
to store coordinates in the inpcrd/restart files. This often happens when
particles diffuse very far away from each other. Make sure you are removing
center-of-mass translation (nscm /= 0) or check if you have multiple, mobile
molecules that have diffused very far away from each other. This condition is
highly unusual for non-periodic simulations.
The first 20 lines of heat.rst7:
default_name
19448 0.1000000E+04
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************3069.2897260************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
heat.in content:
heating with backbone restraints
&cntrl
ntx = 1,
ntwx = 5000,
ntwe = 0,
ntwr = 500,
ntpr = 5000,
ioutfm=0,
ntxo=1,
imin = 0,
nstlim = 500000,
dt = 0.002,
ntt = 3,
gamma_ln=1.,
temp0 = 100.0,
nscm = 1000,
ig = -1,
ntc= 2,
ntf = 2,
cut = 1000,
igb=8,
gbsa=3,
surften=0.007,
ntb = 0,
saltcon=0.15,
ntr=1,
restraintmask=".CA,N,C,O | :ADP,MG",
restraint_wt=10.0,
nmropt=1,
&end
&wt
TYPE="TEMP0", istep1=0, istep2=500000,
value1=100., value2=300.,
&end
&wt
TYPE="END",
&end
nscm is set to 1000, ligands are restrained. Also, I cannot watch the trajectory, so I am completely stuck on this issue.
I've tried to run the protein with other ligands and apo form, but they all fail with the same error (| ERROR: I could not understand line 3).
I would appreciate any help and advice. I apply the heating output and input files.
Thanks in advance,
Ildar
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Received on Tue Feb 20 2024 - 22:00:02 PST
