yes it sounds likely that the minimization is not fixing your bad model.
you will need to look at it and determine whether it is reasonable to
minimize or not. you might also try to fix this problem prior to adding
water. a solvent shell can keep things from moving in minimization since it
will act like ice. also, you should not use restraints on the strained
loop. I am not sure if your residue range included that loop or not.
also, it is often suggested on this list that GPUs not be used for
minimization of bad structures. I suggest using the CPU code for that,
maybe it will work better.
these are things that you need to check since you know your project and
system, and people on this list do not.
On Wed, Sep 25, 2024 at 1:13 PM SUBHASMITA MAHAPATRA MAHAPATRA <
phd2101271009.iiti.ac.in> wrote:
> Thank you for your response.
>
> The PDB file was modelled using I-TASSER. There are few bad contacts in
> the modelled loop region which might be the reason for the high energy. I
> thought minimising the system would resolve the problem. Please let me know
> if there is any other way to handle this issue.
>
> The total output file of minimisation is attached for your reference. I
> have tried to minimise the system in two steps. At first, keeping
> restraints and then without it. It can not calculate vdw interaction (with
> restraint) for all the steps. The same is resolved when the restraints were
> removed but it shows LINMIN failure, which creates a problem in the heating
> step.
>
> I hope it is clear now. I have attached the leap.log file for reference.
>
> On Wed, Sep 25, 2024 at 9:44 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> 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)*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
> --
> *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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Received on Wed Sep 25 2024 - 11:00:02 PDT
