normal regarding disulfide bonds

More
2 weeks 3 days ago - 2 weeks 2 hours ago #7607 by cm
cm created the topic: regarding disulfide bonds
i am following this tutorial
cgmartini.nl/index.php/tutorials-general-introduction/proteins
every thing goes fine and i am able for 1 ns production run at 20 fs.
But when i incorporate disulfide bond by using this command ./martinize.py -f p1p2.pdb -o system-vaccum.top -x p1p2-cys-CG.pdb -dssp /usr/local/bin/dssp -p backbone -ff martini22 -cys auto
the linkage are shown in the pdb file.
but after doing this
mdrun -deffnm minimization-vaccum -v -nt 1
i am getting these lines
Wrote pdb files with previous and current coordinates
Step= 29, Dmax= 1.4e-06 nm, Epot= 7.18484e+03 Fmax= 1.13893e+05, atom= 171
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up minimization-vaccum.gro to ./#minimization-vaccum.gro.3#

Steepest Descents converged to machine precision in 30 steps,
but did not reach the requested Fmax < 10.
Potential Energy = 2.7593826e+03
Maximum force = 7.0681455e+03 on atom 535
Norm of force = 6.1231165e+02

how i will solve the problem

.mdp
integrator = steep
dt = 0.02
nsteps = 10
nstxout = 0
nstvout = 0
nstlog = 100
nstxtcout = 100
xtc-precision = 10
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = Protein
tau-t = 1.0
ref-t = 300
if i change the dt value still the same error occured.

And stil i take this as a note and go for the further steps.at the equilibration step(after solvation and neutralization) i am getting core dumped error
due to linc warning.
Is there any other way to form disulfide bond which make the system stable and there will be no lincs warning in the next equilibration step.
Thanking you.
Last Edit: 2 weeks 2 hours ago by cm.

Please Log in or Create an account to join the conversation.

More
1 week 6 days ago #7611 by cm
cm replied the topic: regarding disulfide bonds
after solvation and neutralization at the equilibration step this error is obtained.
define = -DPOSRES
dt = 0.002
nsteps = 25000
nstxout = 0
nstvout = 0
nstlog = 100
nstxtcout = 100
xtc-precision = 10
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = Protein W ION
tau-t = 1.0 1.0 1.0
ref-t = 300 300 300
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau-p = 5.0 5.0
compressibility = 3e-4 3e-4
ref-p = 1.0 1.0
refcoord_scaling = all
this is .mdp file
the following erorr is obtained
relative constraint deviation after LINCS:
rms 28.758862, max 192.661621 (between atoms 66 and 68)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
61 66 82.8 0.5993 10.9340 0.3100
56 58 92.8 0.3120 7.8992 0.3100
66 68 93.1 0.7486 60.0351 0.3100
66 67 146.1 0.6158 4.3898 0.2650
68 70 88.7 0.7891 51.5558 0.3100
269 270 89.7 0.2700 4.5246 0.2700
70 71 91.4 0.6324 3.5975 0.3100
71 72 107.1 0.7286 1.6625 0.3100
75 79 86.3 0.3258 0.3405 0.3100
79 81 45.9 0.3248 0.3879 0.3100
54 56 90.0 0.3300 5.0654 0.3300
59 61 70.0 0.4342 26.8857 0.3100
58 59 90.5 0.3650 16.1927 0.3100
267 268 90.6 0.2700 2.5395 0.2700
267 269 60.1 0.2700 5.9743 0.2700
268 269 90.2 0.2699 4.1262 0.2700
268 270 90.9 0.2700 0.6014 0.2700

Back Off! I just backed up step154b_n7.pdb to ./#step154b_n7.pdb.4#

Back Off! I just backed up step154c_n7.pdb to ./#step154c_n7.pdb.4#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)

i have two protein in a water box system.if i even change the no of step same error occur.i have also minimized the system upto 50000 step the same error happening.
can anyone please suugest me how i can solve the problem.
thanking you

Please Log in or Create an account to join the conversation.

More
1 week 6 days ago - 1 week 6 days ago #7612 by peterkroon
peterkroon replied the topic: regarding disulfide bonds
You can try a pre-equilibration with a smaller timestep, such as 10 fs. Note that this will produce a non-physical trajectory (at least, we haven't exactly proven it doesn't), but that doesn't matter since you're not going to use it in your analysis.
Be sure to also run an equilibration at 20fs afterwards.
Last Edit: 1 week 6 days ago by peterkroon.

Please Log in or Create an account to join the conversation.

More
1 week 6 days ago #7613 by cm
cm replied the topic: regarding disulfide bonds
I have already tried a 10 fs time step.still the same error is getting.wheather my . mdp file is correct or not .I mentioned that above.
Thank you so much for your quick reply.

Please Log in or Create an account to join the conversation.

More
1 week 6 days ago #7614 by peterkroon
peterkroon replied the topic: regarding disulfide bonds
Nowhere do you mention using a 10fs timestep.
You can try with 5fs, but if that also doesn't work something is very wrong with your structure.

Please Log in or Create an account to join the conversation.

More
1 week 6 days ago #7615 by cm
cm replied the topic: regarding disulfide bonds
The md run was fine even at 10 fs before adding the disulfide bond.
But when I added disulfide bond(command mention above) by using auto cys.Linc error obtained at equlibration step.

Please Log in or Create an account to join the conversation.

More
1 week 6 days ago #7616 by peterkroon
peterkroon replied the topic: regarding disulfide bonds
Could you post the line from your ITP with the bonded parameters for the cystein bridge? And the distance between them in the original PDB?

Please Log in or Create an account to join the conversation.

More
1 week 6 days ago #7618 by cm
cm replied the topic: regarding disulfide bonds
thanks a lot for your valuable suggestion.Forming the disulfide bonds separately i have solve the problem.Now the equlibration is ok.

Please Log in or Create an account to join the conversation.

More
1 week 5 days ago #7619 by peterkroon
peterkroon replied the topic: regarding disulfide bonds
Good to hear. We however, are still interested in the itp as it was produced by martinize. We need to know whether there's a bug there.

Please Log in or Create an account to join the conversation.

Time to create page: 0.099 seconds