if the energies are ok but coordinates not, perhaps the system is shifted
far from the origin. try using netcdf binary outputs.
section 21.6.3 of the Amber23 manual.
On Wed, Feb 21, 2024 at 9:59 AM Ildar Garipov <
garipov_ildar_from.tp.bii.a-star.edu.sg> wrote:
> I've tried to equilibrate apoprotein without any ligand and with another
> ligand (ADP with MG), but I have the same error for all systems (ERROR: I
> could not understand line 3).
>
> Minimization wents well and converges in 31 steps. Heating finishes
> without any issue (at least heat.out doesn't report any error at the end).
> But coordinate files .nc and .rst7 are corrupted for some reason.
>
> Ligands (ADP, PEP) topologies were made by antechamber with GAFF (just
> like in this tutorial
> https://ambermd.org/tutorials/basic/tutorial4b/index.php). But I have the
> same problem with apoenzyme, so I suppose the problem does not occur by
> ligands. Furthermore, they are restrained during the heating and can't fly
> away from their sites.
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Wednesday, February 21, 2024 7:03 PM
> *To:* Ildar Garipov <garipov_ildar_from.tp.bii.a-star.edu.sg>; AMBER
> Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] issue performing heating of protein in implicit
> solvent
>
> This email is from a sender external to A*STAR. If you are unsure of the
> content, please check the source before you respond.
>
> First, make sure your protocol works without ligands. If it does, I would
> check the ligand force field parameters or the initial coordinates. You
> don't mention how you generated either of these. Check the heating output
> and look carefully at the first step to see if high energies are reported.
> Look at the output from minimization as well.
>
>
> On Wed, Feb 21, 2024, 12:39 AM Ildar Garipov via AMBER <amber.ambermd.org>
> wrote:
>
> 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 Wed Feb 21 2024 - 07:30:02 PST
