[gmx-users] Segmentation fault (core dumped) error during minimization

[Justin Lemkul]

On 4/28/20 5:08 AM, Elham Taghikhani wrote:
> Hi
> As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom.
> And the atom which errored  during minimization it's the atom that bound covalently to a ligand. I think there is something wrong with the bond length between N of amino acid and the C of the ligand. How can I find the correct bond length?
>

You'll have to provide more information about how you parametrized this 
covalent ligand. This is a far different case from a "normal" 
protein-ligand complex and requires very careful force field 
parametrization, including the linkage itself and any impacts that may 
have on associated protein terms. In this case, I don't see how you can 
assess the stability of the ligand topology by itself, as you said you 
had. Please explain in greater detail.

-Justin

>> On Apr 20, 2020, at 1:08 AM, Elham Taghikhani <elham802011 at yahoo.com> wrote:
>>
>> Thank you
>> I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom.
>> Could you explain how can I observe bad contacts in the structure?
>> I even tried the different box size but it didn't work.
>> Both ligand and protein are ok with minimization separately.
>>
>>
>>>> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani <elham802011 at yahoo.com> wrote:
>>>>
>>> 
>>> Hi
>>>   
>>> I am simulating a protein-ligand system, using oplss force field but i got this error during minimization.
>>>
>>> Steepest Descents:
>>>     Tolerance (Fmax)   =  1.00000e+03
>>>     Number of steps    =        50000
>>> Step=    0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996
>>> Segmentation fault (core dumped)
>>>
>>> and this is my mpd file:
>>> ; LINES STARTING WITH ';' ARE COMMENTS
>>> title		    = Minimization	; Title of run
>>>
>>> ; Parameters describing what to do, when to stop and what to save
>>> integrator	    = steep		; Algorithm (steep = steepest descent minimization)
>>> emtol		    = 1000.0  	; Stop minimization when the maximum force < 10.0 kJ/mol
>>> emstep          = 0.01      ; Energy step size
>>> nsteps		    = 50000	  	; Maximum number of (minimization) steps to perform
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
>>> nstlist		    = 1		        ; Frequency to update the neighbor list and long range forces
>>> cutoff-scheme   = Verlet
>>> ns_type		    = grid		    ; Method to determine neighbor list (simple, grid)
>>> rlist		    = 1.2		    ; Cut-off for making neighbor list (short range forces)
>>> coulombtype	    = PME		    ; Treatment of long range electrostatic interactions
>>> rcoulomb	    = 1.2		    ; long range electrostatic cut-off
>>> vdwtype         = cutoff
>>> vdw-modifier    = force-switch
>>> rvdw-switch     = 1.0
>>> rvdw		    = 1.2		    ; long range Van der Waals cut-off
>>> pbc             = xyz 		    ; Periodic Boundary Conditions
>>> DispCorr        = no
>>> Can anyone suggest how to troubleshoot this error?
>>> The system is nuetralized.
>>>   
>>> Thank you in advance.
>>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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