since your energy is high, you'll want to think about possible causes of
the high energy in order to do some troubleshooting.
some possible questions you might consider are:
- what is the source of the original structure given to tleap? could any
portions be unreliable?
- were there any missing atoms, or other issues that tleap reported? did
you check how tleap built these atoms, and if they are reasonable?
- did you use any non-standard force field libraries?
- did you create your input files using an established, tested protocol,
such as ones from the ambermd.org tutorials, or from a published relaxation
procedure such as the one published by Dan Roe?
- did you look at your entire minimization output file, rather than just
the part that you copied to the email? For example, did you check step 1,
and see if that gives you clues about the source of the problem?
On Wed, Sep 25, 2024 at 11:48 AM SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <
amber.ambermd.org> wrote:
> Hi,
>
> I am trying to simulate a protein-protein complex with 490 residues. The
> solvated prmtop and inpcrd files were generated using tleap with periodic
> boundary 14.0. However, in the minimisation step, I see LINMIN failure,
> which creates the following error in the heating step.
>
> NSTEP = 200 TIME(PS) = 0.400 TEMP(K) =********* PRESS =
> 0.0
>
> Etot = ************** EKtot = ************** EPtot =
> **************
>
> BOND = ************** ANGLE = 386725.8079 DIHED =
> 27473.9232
>
> 1-4 NB = 0.0000 1-4 EEL = 0.0425 VDWAALS =
> **************
>
> EELEC = -262856.4676 EHBOND = 0.0000 RESTRAINT =
> **************
>
> EAMBER (non-restraint) = **************
>
>
> Please find the attached files for your reference.
>
>
> Kindly help me in this regard.
>
>
> Thank you
>
> --
> *Yours Sincerely*
> *Subhasmita Mahapatra*
> *Ph.D. Scholar (PMRF)*
> *Computational Biophysics Group*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology, Indore*
> *Madhya Pradesh, India (453552)*
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 25 2024 - 09:30:02 PDT
