normal Clarifiaction about chlrophyll a molecule Coarsed grained topology file

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7 months 3 weeks ago #8867 by saini
I could not resolve this issue yet. force during EM is 1000
emtol = 1000 in minimization.mdp file

I tried by decrease the timestep and tau_t value. in this time it ran 13ns NVT after that show LINCS warning.

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7 months 3 weeks ago #8868 by vainikka
Decrease the emtol value to 10 (standard value in the mdp settings) and work your way through the list again.

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7 months 2 weeks ago #8869 by saini
Thank you vainikka for your kindly reply. but when i am using emtol value 10
energy is not minimized it shows this

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 252 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.3363615e+06
Maximum force = 1.0116125e+03 on atom 9951
Norm of force = 1.0875615e+01

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7 months 2 weeks ago #8870 by vainikka
Nothing to worry about, it's just as the message says: GROMACS could not reach the emtol value you put it, but it tried to get as close to it as possible.

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7 months 2 weeks ago #8871 by saini

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7 months 1 week ago #8882 by saini
Dear Martini users
I want to do loose pressure copuling, but i confused should i increase or decrease tau_p value? and what other perameter will change for loose pressure coupling?

my mdp file value are here

tcoupl = Berendsen
tc-grps = cla_lipids sol
tau_t = 2.0 2.0
ref_t = 293 293
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 1
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

I increase the tau_p value for loose coupling tau_p = 2 ps, then submit job but it show error like

Fatal error:
Unexpected cudaStreamQuery failure: an illegal memory access was encountered


my comand line is

gmx mdrun -v -s 128cla_npt_loose_coup.tpr -deffnm test -ntmpi 1 -ntomp 4 -pin on -pinoffset 160 -pinstride 1 -tunepme no -nstlist 400 -nb gpu -bonded gpu -pme gpu

please correct me where i am doing mistake?

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6 months 3 weeks ago #8902 by saini
Dear Martini users,
I am trying to convert atomistic structure into coarse grained (CG) of chlorophyll a (CLA) molecule by using martinize.py script.

it did not work for CLA molecule. i downloaded CLA molecule .sdf file from RCSB website then by using avogadro i save this CLA_ideal.sdf file in pdb format.

the command line that i am using is
python martinize.py -f CLA_ideal.pdb -o single_cla.top -x cla-CG.pdb -dssp ./dssp -p backbone -ff martini22

after ran this command i got this on terminal

INFO MARTINIZE, script version 2.6
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 1 chains:
INFO 1: (Unknown), 137 atoms in 1 residues.
INFO Removing HETATM chain consisting of 1 residues.
INFO Total size of the system: 0 residues.
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
INFO Written 0 ITP file
INFO Output contains 0 molecules:
INFO Written topology files
INFO Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.

but this script is running for other molecules pdb file.
Please suggest me, how can i fix this problem.

if there is All atom pdb or CG CLA gro is available on any website please let know where i can get CLA molecule CG gro file.

Any help/suggestions on what I can do? Feedback would be much appreciated.

Thank you.

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6 months 3 weeks ago #8905 by vainikka
martinize requires a mapping file to figure out which atoms go where. In the case of CLA you already have the correct topology (at least I assume so, since you were provided with a download link earlier in this thread), so all you need to do is to put a right number of beads in to a box, refer to the CLA.itp in your .top file and minimize.

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6 months 2 weeks ago #8910 by saini
I could not resolve it yet. i Just kept 23 beads in a box and the beads name i set according to chlorophyll_a.iitp file from this cite cgmartini.nl/index.php/psii
my 1cla.gro with 23 beads is like that
CLA
23
1CLA NA 1 1.902 12.059 4.639 -0.2338 0.0458 0.0760
1CLA CHA 2 1.998 12.228 4.728 -0.2383 -0.2153 -0.0255
1CLA NB 3 2.033 12.093 4.481 0.4977 -0.0777 0.1318
1CLA CHB 4 1.958 11.859 4.582 0.1736 0.0644 -0.4561
1CLA NC 5 1.975 11.979 4.822 -0.1787 0.2577 -0.4076
1CLA CHC 6 1.999 12.184 4.962 -0.1448 -0.2055 0.3604
1CLA ND 7 2.024 11.755 4.797 -0.3473 0.2860 0.0958
1CLA CHD 8 1.983 11.625 4.442 0.0938 -0.2695 0.0421
1CLA C1A 9 2.085 11.493 4.684 -0.4512 -0.4162 0.1746
1CLA C2A 10 1.962 11.898 4.347 0.2372 -0.2194 -0.3866
1CLA C1B 11 2.184 12.196 4.288 0.0744 0.1325 -0.1576
1CLA C2B 12 2.178 12.007 4.120 -0.2895 0.0432 0.3014
1CLA C1C 13 2.169 12.274 4.567 0.0133 0.1509 -0.0053
1CLA C2C 14 2.094 12.452 4.758 -0.4154 -0.0706 -0.3372
1CLA T1 15 2.032 11.845 5.065 0.1887 0.3553 0.2883
1CLA C1D 16 2.088 12.032 5.208 -0.3525 0.1092 -0.3116
1CLA C2D 17 1.940 12.303 5.176 0.1154 -0.4853 0.1600
1CLA T2 18 2.027 12.307 5.367 -0.0345 0.3314 -0.5669
1CLA T3 19 1.882 12.494 4.873 0.0969 0.0074 -0.1357
1CLA T4 20 1.749 12.670 4.871 0.0834 0.4260 -0.1194
1CLA T5 21 1.726 12.939 4.653 0.2145 0.0221 -0.0616
1CLA T6 22 1.916 13.084 4.219 0.4054 -0.0219 0.2319
1CLA MG 23 1.618 13.394 3.956 -0.0895 -0.0303 0.0300
10 10 10

Mg is not in the center, it is at the tail.
but it should be in center acc to this paper:

Atomistic and Coarse Grain Topologies for the Cofactors Associated
with the Photosystem II Core Complex
Djurre H. de Jong, Nicoletta Liguori, Tom van den Berg, Clement Arnarez, Xavier Periole,* and Siewert J. Marrink* ,

DOI : 10.1021/acs.jpcb.5b00809

when i am using martinize.py it convert only protein chains into CG beads other molecule like chlorophyll and lipids are not converted in CG beads.

is this script work only for protein? or is there another method to build CG structure of lipids and other biomolecules instead of protein?

I am using this command:

python martinize.py -f 1cla.pdb -o 1cla.top -x 1cla-CG.pdb -dssp ./dssp -p backbone -ff martini22
but no output residue in the output file.

Please suggest me something how can i fix this problem?

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6 months 2 weeks ago #8911 by saini
Is there any different script for small bio-organic molecules to convert all atom to CG structure? please provide the link and command if it is there.

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6 months 2 weeks ago #8912 by peterkroon
Hi Saini,

you could give Martinize2 a try ( github.com/marrink-lab/vermouth-martinize , installation instructions also there). Note that it is still under development, so you may encounter issues. In addition, you may need to add the required datafiles for your molecules, although everything for proteins should be there. Unfortunately there are no tutorials/documentation available yet, so you'll need to take a look at how the current molecules are implemented and take it from there. You can find those files in the folder vermouth/data.

Good luck :)

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6 months 2 weeks ago #8913 by saini
OK, i will check it.
Thank you so much.

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2 months 2 weeks ago #9093 by saini
Dear Martini Users,
I am mapping chlorophyll a molecule (from all atom to coarsed grained structure) by using the itp file downloaded from this below site-

www.cgmartini.nl/index.php/60-downloads/...c-topologies?start=6

All Topologies for the cofactors associated with the Photosystem II are given in the topologies.zip file.

the chlorophyll_a-CG.itp is this

; Chlorophyll-A Coarse-grained
;
; If using this topology, please site:
; De Jong et al, J. Phys. Chem. B, 2015, 119 (25), pp 7791–7803, doi:10.1021/acs.jpcb.5b00809
;
;MODIFIED CLA_CG topology JANUARY 2014, modiefied dihedrals to keep the rings flat and a few different exclusions
[ moleculetype ]
; molname nrexcl
CLA 1

[ atoms ]
;id type resnr residu atom cgnr charge
;mapping to keep molecule symmetric and use small beads.
;Eight beads in the ring preserves symmetry better then 6.
;Eight beads in the ring gives more rigid molecule
;Eight bead ring is to heavy.
1 SP3 1 CLA NA 1 -0.25
2 SC3 1 CLA CHA 2 0.00
3 SP3 1 CLA NB 3 -0.25
4 SC3 1 CLA CHB 4 0.00
5 SP3 1 CLA NC 5 -0.25
6 SC3 1 CLA CHC 6 0.00
7 SP3 1 CLA ND 7 -0.25
8 SC3 1 CLA CHD 8 0.00
9 SC3 1 CLA C1A 9 0.00
10 SC3 1 CLA C2A 10 0.00
11 SC3 1 CLA C1B 11 0.00
12 SC3 1 CLA C2B 12 0.00
13 SC4 1 CLA C1C 13 0.00
14 SNa 1 CLA C2C 14 0.00
15 Na 1 CLA T1 15 0.00
16 SC3 1 CLA C1D 16 0.00
17 SC3 1 CLA C2D 17 0.00
18 Na 1 CLA T2 18 0.00
19 C3 1 CLA T3 19 0.00
20 C1 1 CLA T4 20 0.00
21 C1 1 CLA T5 21 0.00
22 C1 1 CLA T6 22 0.00
23 SQ0 1 CLA MG 23 1.00

[ bonds ]
; bonds between beads
; The bonds are finetuned against a backmapped gromos simulation
1 9 1 0.273 30000.0
9 10 1 0.298 23000.0
1 10 1 0.318 25000.0
3 11 1 0.274 25000.0
3 12 1 0.319 23000.0
11 12 1 0.29 21000.0
5 13 1 0.24 25000.0
5 14 1 0.355 21000.0
6 14 1 0.28 25000.0
13 14 1 0.29 20000.0
14 15 1 0.305 10000.0
7 17 1 0.250 25000.0
7 16 1 0.250 22000.0
16 17 1 0.255 25000.0
17 18 1 0.330 5000.0
18 19 1 0.44 6000.0
19 20 1 0.460 12000.0
20 21 1 0.505 12000.0
21 22 1 0.510 12000.0

[ constraints ]
; constraints between beads
; The contraints are finetuned against a backmapped gromos simulation
1 2 1 0.223
2 3 1 0.225
3 4 1 0.225
4 5 1 0.221
5 6 1 0.223
6 7 1 0.220
7 8 1 0.226
8 1 1 0.224
1 5 1 0.476
3 7 1 0.474
2 4 1 0.448
4 6 1 0.441
6 8 1 0.443
8 2 1 0.444
1 23 1 0.238
3 23 1 0.238
5 23 1 0.238
7 23 1 0.238

[ angles ]
; angles between atoms
; The angles are finetuned against a backmapped gromos simulation
2 1 9 2 121 2000
2 1 10 2 64 900
1 10 9 2 53 1600
4 3 11 2 119 2000
4 3 12 2 66 600
3 12 11 2 54 1500
1 2 3 2 98 1000
3 4 5 2 97 1000
5 6 7 2 99 1000
7 8 1 2 99 1000
4 5 13 2 79 1200
5 13 14 2 85 1500
16 17 18 2 111 100
6 14 15 2 74 100
5 14 15 2 104 50
17 18 19 2 152 40
18 19 20 2 143 40
19 20 21 2 180 400
20 21 22 2 178 500
8 7 16 2 78 100
8 7 17 2 110 450
6 7 16 2 116 800
6 7 17 2 76 750


[ dihedrals ]
; No proper-dihedrals are defined: the tail is very linear already
; impropers, to keep molecule flat and stable
1 3 7 10 2 0.0 500.0
1 3 7 9 2 0.0 500.0
3 5 1 11 2 0.0 500.0
3 5 1 12 2 0.0 500.0
5 6 13 4 2 0.0 500.0
5 6 14 4 2 0.0 500.0
;To keep ND part straight
1 8 7 16 2 -157.0 500.0
7 8 16 17 2 43.5 500.0
1 5 8 17 2 -159.0 1000.0
;To keep T1 in trans position
5 6 14 15 2 -137.0 500.0

[ exclusions ]
;Almost everything is excluded because it is such a cramped molecule
; First bonded neighbors are already excluded
1 2 3 4 5 6 7 8
2 3 4 5 6 7 8 9 10 11 12
3 4 5 6 7 8
4 5 6 7 8 11 12 13 14
5 6 7 8 14
6 7 8 13 14 15 16 17
7 8
8 9 10 16 17
9 11 12 16 17
10 11 12 16 17
11 13 14
12 13 14
13 15 16 17
14 16 17
15 16 17 ; remove if trouble
16 18
23 2 4 6 8

; To be inserted in the atomistic Gromos topology
; Atoms 29 33 45 47 50 57 60 62 are double mapped. Halve their atomistic mass!!
;[ mapping ]
;1 60 61 62
;2 60 58 59 57
;3 57 51 50
;4 50 48 49 47
;5 47 46 45
;6 45 34 33
;7 33 32 29
;8 29 30 31 62
;9 63 64
;10 65 66 67
;11 55 56
;12 52 53 54
;13 42 43 44
;14 35 40 41
;15 36 37 38 39
;16 26 25
;17 26 28
;18 24 23 22 21 20
;19 19 18 17 16
;20 15 14 13 12 11
;21 10 9 8 7 6
;22 5 4 3 2 1
;23 67

#ifdef POSRES
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
2 1 1000 1000 1000
3 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
11 1 1000 1000 1000
12 1 1000 1000 1000
13 1 1000 1000 1000
14 1 1000 1000 1000
15 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
18 1 1000 1000 1000
19 1 1000 1000 1000
20 1 1000 1000 1000
21 1 1000 1000 1000
22 1 1000 1000 1000
23 1 1000 1000 1000
#endif

There are first bond is in bead 1 and 9, second one in between 9 and 10 etc.

There are bonds missing in between the beads 1 and 2, 2 and 3, 3 and 4 etc.. in the ring part of the chlorophyll a molecule but constraint is there.

Is it a typo that bonds are missing and constrained only or is it constructed intentionally like this? if it is constructed intentionally like this please let me know what is the reason behind ?

Thank you.

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2 months 2 weeks ago #9094 by bart
This seems to be intentional. The constraints replace the bonds in the aromatic rings so the highest frequency (limiting the integration timestep) is much lower. A similar thing occurs in some atomistic fields. Where the hydorgens are constrained (or virtual sites can be used with the same intent).

PS
I did not check the itps line by line to check for possible mistakes. I just wanted to explain what the general approach is.

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2 months 2 weeks ago #9095 by saini
Thank you so much for clarifying.

Can someone please confirm if the itp file present in the website is correct?

website link-
www.cgmartini.nl/index.php/60-downloads/...c-topologies?start=6

the below link for topolozy of all PSII cofactor zip file-

www.cgmartini.nl/images/parameters/ITP/topologies.zip

Thank you.

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1 month 1 week ago #9127 by saini
Dear Martini Users,
I am using Chlorophyll-a coarse grained itp that is given in the below website link
cgmartini.nl/index.php/force-field-parameters/others
I have added 8 cla in lipid bilayer. It is work fine but when i am adding more CLA like 16 or 32 CLA in the lipid bilayer, after 400 0r 500ns NPT equilibration density suddenly increased and CLA molecules start vibrating at one position, CLA molecules position not changing after density increment.
the following mdp file i am using:
title = Martini
integrator = md
tinit = 0.0
dt = 0.010
nsteps = 250000000 ;2500ns
nstcomm = 100
comm-grps = cla_lipids sol
nstxout = 0
nstvout = 0
nstfout = 0
nstlog =20000 ;200 ps
nstenergy =20000
nstxtcout =20000
xtc_precision =20000
xtc-grps = cla_lipids sol
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = PME
pme-order = 4
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Cut-off
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = cla_lipids sol
tau_t = 1.0 1.0
ref_t = 293 293
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 3
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 105
gen_seed = 548628
constraints = none
constraint_algorithm = Lincs
lincs_order = 4
lincs_warnangle = 30


Density not increased in the case of 8 CLA but for 16 and 32 CLA case density suddenly increase. Please let me know why density is increased suddenly, what is going wrong? It will be great help for me.

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1 month 1 week ago #9128 by saini
Dear Martini Users,
I am using Chlorophyll-a coarse grained itp that is given in the below website link
cgmartini.nl/index.php/force-field-parameters/others
I have added 8 cla in lipid bilayer. It is work fine but when i am adding more CLA like 16 or 32 CLA in the lipid bilayer, after 400 0r 500ns NPT equilibration density suddenly increased and CLA molecules start vibrating at one position, CLA molecules position not changing after density increment.
the following mdp file i am using:
title = Martini
integrator = md
tinit = 0.0
dt = 0.010
nsteps = 250000000 ;2500ns
nstcomm = 100
comm-grps = cla_lipids sol
nstxout = 0
nstvout = 0
nstfout = 0
nstlog =20000 ;200 ps
nstenergy =20000
nstxtcout =20000
xtc_precision =20000
xtc-grps = cla_lipids sol
cutoff-scheme = verlet
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = PME
pme-order = 4
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Cut-off
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = cla_lipids sol
tau_t = 1.0 1.0
ref_t = 293 293
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 3
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 105
gen_seed = 548628
constraints = none
constraint_algorithm = Lincs
lincs_order = 4
lincs_warnangle = 30


Density not increased in the case of 8 CLA but for 16 and 32 CLA case density suddenly increase. Please let me know why density is increased suddenly, what is going wrong? It will be great help for me.

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