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amino acid bonds
- yamahdi
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as I have understood the bonds between beads of following amino acids THR, VAL, ILE,are different from the others and are weaker. I think the root of linc warning mentioned in my previous question may be here. would you pleaes help me?
thanks for your kind help in advance
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- xavier
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This basically means that the bonds are "strong" and I am not sure how that relates to the lincs warnings!
XAvier.
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- yamahdi
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now where may has been my mistake resulting in LINCS WARNING in first step of in vacuum simulation of some proteins?!!!
as I have see the error is about over load and pressure in beads of Val, THR and Ile leading in big changes in angles and...!
thanks from your kind help in advance
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- xavier
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you experience lincs warnings during minimization of your CG protein!
One question: does the minimization gets to completion?
It is probable that your starting structure contains some bad contact resulting in strong forces ... did you check for such bad contact?
It might be good that you describe your protocol in more details
XAvier.
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- yamahdi
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2- it seems VMD doesn't show any bad contact!
3- the beads at which warning error has been seen are exactly the beads of VAL, THR, ILE.
4- We exactly have done the steps of toturial at your site and have used the seq2itp and so ... which are located at the web.
thanks
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- xavier
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Try to visualize both atomistic and CG pdb/gro files and make sure that all atoms are present and that nothing funky happens during the conversion. It does not make much sense that the minimization does not go through ...
XAvier.
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- siewert
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Therefore, during minimization, it is better to convert the constraints to harmonic bonds, even when they are stiff. Once you continue with MD, you should switch back to constraints again unless you want to use a small time step.
It is all described in the FAQ, under problems 'my simulations keep crashing ...'
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- yamahdi
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we successed to have a simulation after removing constrains. then short minmization step has been done and also a short MD. but we have a problem with 2 LYS amino acids which have been separated from the model and are observed in a far distance.
there is also one question which I am not sure if have any effect on the simulation or not: for desulfide bonds as 'i have been understood, you have only presented bond's lenght and strenght and noting has been mentioned about dihedrals or angle of bond. Is it OK or there is some point I have missed?!
would you pleaes help me where may mistake?
thanks in advance
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- xavier
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Congratulations :))Hi
we successed to have a simulation after removing constrains. then short minmization step has been done and also a short MD.
I am not sure what you mean here. Could it simply be a periodic boundary condition effect?but we have a problem with 2 LYS amino acids which have been separated from the model and are observed in a far distance.
I do not understand what is your problem here!there is also one question which I am not sure if have any effect on the simulation or not: for desulfide bonds as 'i have been understood, you have only presented bond's lenght and strenght and noting has been mentioned about dihedrals or angle of bond. Is it OK or there is some point I have missed?!
Defining a disulfide bridge in the topology as been a bond with the correct equilibrium distance and force constant is indeed fine!
XAvierwould you please help me where may mistake?
thanks in advance
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- yamahdi
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- xavier
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Good luck for the rest.
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- roshanak
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i have a similar problem in minimization step. i remove constraints from .itp file and i do a successful minimization by short time step (dt=0.001 ps ) for 1 ns.
(but i must tell that beginning energy of my system was very high in the potential energy analysis before that reachs a negative amount in minimization.)
i try to do equilibration step. when i convert the constraints to .itp file, i receive lincs warning again. i try do this step without constraints, but i receive this error:
Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
G96Angle of 2564 missing 1
Program mdrun, VERSION 4.5.5
Source code file: domdec_top.c, line: 173
Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
i search for this error and i find page of gromacs documentation about blowing up. but i don't find my solution.
can you help me?
thank you
(my system includes 5 peptide to form of pantagonal in center of dppc bilayer.)
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- peterkroon
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It seems that your starting configuration is just not good/stable enough. Check for clashing atoms.
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- roshanak
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my commands:
$ gmx editconf -f 1.pdb -princ -o ax.gro
$ gmx editconf -f ax.gro -rotate 0 90 0 -o az.gro
$ gmx editconf -f az.gro -bt cubic -center 5.7 4.036 8 -box 10 10 12 -o box1.gro (and i do it for other boxs with their cordinates)
$./martinize2.6.py -f box1.gro -o topol1.top -x box1CG.pdb -dssp /usr/local/bin/dssp -p backbone -ff martini22 (i do it for box2-3-4 & 5)
$ gmx editconf -f box1CG.pdb -o box1CG.gro
$ cat box1CG.gro box2CG.gro box3CG.gro box4CG.gro box5CG.gro> a5gonCG.gro
$./insane.py -f a5gonCG.gro -o aurein-dppct.gro -p topolt.top -pbc squar
e -box 10,10,12 -l DPPC -sol W -dm 0 (topolt.top includes .itp files without constraints)
$ gmx grompp -f minimization1fDPOS.mdp -c aurein-dppct.gro -p topolt.top -o minimt.tpr
$ gmx mdrun -deffnm minimt -nt 4 -v
$ gmx make_ndx -f minimt.gro -o index.ndx
$ grompp -f equilibration.mdp -c minimt.gro -p topolt.top -o equ.tpr -n in
dex.ndx
$ mdrun -deffnm equ -nt 2 -v
minimization.mdp:
;define = -DFLEXIBLE
define = -DPOSRES
integrator = steep ; Run steepest descent energy minimization algorithm
dt = 0.001
nsteps = 1250000 ; Number of steep steps to run
nstcomm = 100
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 100 ; Output frequency for energies to log file
nstenergy = 100 ; Output frequency for energies to energy file
nstxtcout = 1000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps =
energygrps = System
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
cutoff-scheme = group
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
equilibration.mdp:
define = -DPOSRES
;define = -DFLEXIBLE
integrator = md
dt = 0.001
nsteps = 5100000
nstcomm = 100
comm-grps = Protein_DPPC W
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000 ; Output frequency for energies to log file
nstenergy = 100 ; Output frequency for energies to energy file
nstxtcout = 1000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps =
energygrps = Protein_DPPC W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
;cutoff-scheme = group
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
tcoupl = v-rescale
tc-grps = Protein DPPC W
tau_t = 1.0 1.0 1.0
ref_t = 323 323 323
Pcoupl = berendsen ; berendsen ; parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12 ; 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4 ; 3e-4
ref_p = 1.0 1.0 ; 1.0 1.0
refcoord-scaling =com
gen_vel = yes
gen_temp = 323
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
i setup my system and do minimization step in my laptop (gromacs 2016). but i make equ.tpr and run equilibration in camputer with gromacs 4.5.5 (becaue it takes a long time)
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- roshanak
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- peterkroon
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1) your gromacs version is truly ancient. Do you have a good reason for not upgrading?
2) I'm not sure you need 3 different TC groups. If the protein is properly embedded in the membrane I would merge it with the lipid group, and if it's really in both solvent and membrane I would either use just 1 TC group, or 3 like you have now.
Did you check your initial structure for clashes and/or missing atoms in the protein?
And did your minimization converge? Or did it run out of steps?
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- roshanak
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2. I want to study behavior of this pentagonal into the membrane. at the first, I put the peptides in center of membrane.I want to see what'll happen. Whether the water penetrates into the membrane? I thought that must be 3 group. Is it wrong?
Minimization without constraints was successful and it converged.
In my initial structure seems some lipids are very near the peptides. that seems the some lipid's beads stick to some of peptide's beads. i do this step with insane.py
thank you
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- roshanak
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I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
Potential energy, temperature and pressure analysis show very very small fluctuations (almost linear). Is it normal?
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- roshanak
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I forget to tell that i look at the files before insane.py and after minimization, all atoms exist.
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- peterkroon
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Can you find for me the shortest distance between any two beads after the minimization?
>I read in other post, about increasing lincs order (from 4 to 8). is it reasonable in my case?
I might help, but the effect is more pronounced if there are a lot of constraints in your system (i.e. polarizable water)
>I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
What does this mean?
>Potential energy, temperature and pressure analysis show very very small fluctuations (almost linear). Is it normal?
Yes.
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