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 <elham802...@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 <elham802...@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.


--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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