[gmx-users] Segmentation fault (core dumped) error during minimization
Justin Lemkul
jalemkul at vt.edu
Wed Apr 29 18:29:56 CEST 2020
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
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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