[gmx-users] DispErsion correction
jalemkul at vt.edu
Tue Nov 13 00:50:49 CET 2018
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
> 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?
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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