[gmx-users] DispErsion correction

[Justin Lemkul]

On 11/8/18 10:58 AM, Farial Tavakoli wrote:
> Dear Justin and Dallas
>
> Thank you for your replying
>
> I have another problem in minimizing and NVT run of my complex, including a
> protein and a peptidic ligand which the ligand has 2 phosphotyrosine
> residues. I generated a topology file of ligand using ff14sb in ambertools
> 16 and then converted the .inpcrd and .prmtop files in .gro and .top files
> using acpype python script. The protein topology was generated using
> amber99sb ff in GROMACS.
> Then, I cited to gromacs manuscript in order to generate an .itp file of
> ligand from .top file and generated .itp file by removing the header and
> footer of .top file in such a way that .itp file starts with :
> [ moleculetype ]
> ;name            nrexcl
>   mig               3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
> bond_type
>       1   N3     1   THR     N    1     0.181200     14.01000 ; qtot 0.181
>       2    H     1   THR    H1    2     0.193400      1.00800 ; qtot 0.375
> .
> .
> .
> and ends with
>      120    123    122    132      1   180.00   4.18400   2 ;      C-
> CD-     N-    CA
>     132    135    134    136      1   180.00  43.93200   2 ;     CA-
> O-     C-   OXT
> then, modified the complex.gro and .top files according to the tutorials in
> gromacs, I Minimized the complex by issuing this coomand:
> gmx grompp -f em.mdp -c solv-ions.gro -p topol.top -o em.tpr
> gmx mdrun -v -defnm em
> but noticed that the minimization ended soon :
>
> Steepest Descents converged to machine precision in 80 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -6.5639856e+05
> Maximum force     =  7.0647156e+04 on atom 5256
> Norm of force     =  5.8775842e+02
>
> and when performed the NVT run , faced to this error:
>
> starting mdrun 'Protein in water'
> 200000 steps,    400.0 ps.
> step 0
> Step 5, time 0.01 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.016999, max 0.734404 (between atoms 5258 and 5261)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     5258   5261   90.0    0.0960   0.1665      0.0960
>     5283   5286   90.0    0.0960   0.1425      0.0960
> Wrote pdb files with previous and current coordinates
> .
> .
> .
> It should be noted that atoms 5258 and 5261 are related to sol molecules.
> TIP3P water model was selected for amber99sb force field.
> Would you please advice and guild me how should I resolve this problem?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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