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- satnamphysics
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10 years 10 months ago #1709
by satnamphysics
Related to gro file of surfactant was created by satnamphysics
I have to simulate DPPC+Water. For that I have to use a
surfactant SDS. I have downloaded .itp file of
surfactants. But I need gro file(coordinate file). How
I get that file for SDS. I shall be thankful to you.
surfactant SDS. I have downloaded .itp file of
surfactants. But I need gro file(coordinate file). How
I get that file for SDS. I shall be thankful to you.
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- djurre
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10 years 10 months ago #1710
by djurre
Replied by djurre on topic Related to gro file of surfactant
For this purpose there we have a great tool, that creates a structure from a topology:
http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/266-molmaker
http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/266-molmaker
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- satnamphysics
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10 years 10 months ago #1711
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
Thanks
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- satnamphysics
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10 years 10 months ago #1713
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
When I run that program following problem occurs
File "molmaker.py", line 40
init-lambda =-1
SyntaxError: invalid syntax
Kindly help me to solve this...
File "molmaker.py", line 40
init-lambda =-1
SyntaxError: invalid syntax
Kindly help me to solve this...
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- mnmelo
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10 years 10 months ago #1714
by mnmelo
Replied by mnmelo on topic Related to gro file of surfactant
Hi Satnam,
That error is fishy, in the sense that in the file you should have downloaded line 40 reads
"init-lambda = 0"
Maybe you've got a corrupted download? (the md5 hash of the script file is 3b0e5d3b9936bb4a8f1f318eab22f22a)
Or maybe you modified the script in some way to render it unstable? That entire section of the script (lines 27 to 48) is user-modifiable, but since the lines are enclosed in triple quotes, python should not even try to interpret them.
Finally, I got the script running under python 2.7. As far as I'm aware there should be no problem in running it under 2.6 (EDIT: for python 2.6 you'll need to install the argparse module; using pip or easy_install will do), but I can't vouch for python3.
Please let me know if this information helps you solving the issue.
Manel
That error is fishy, in the sense that in the file you should have downloaded line 40 reads
"init-lambda = 0"
Maybe you've got a corrupted download? (the md5 hash of the script file is 3b0e5d3b9936bb4a8f1f318eab22f22a)
Or maybe you modified the script in some way to render it unstable? That entire section of the script (lines 27 to 48) is user-modifiable, but since the lines are enclosed in triple quotes, python should not even try to interpret them.
Finally, I got the script running under python 2.7. As far as I'm aware there should be no problem in running it under 2.6 (EDIT: for python 2.6 you'll need to install the argparse module; using pip or easy_install will do), but I can't vouch for python3.
Please let me know if this information helps you solving the issue.
Manel
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- satnamphysics
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10 years 10 months ago #1715
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
Dear Manel,
I have downloaded that file again. At this time when I run program then following problem occur.It is also giving the option of default force fields of GROMACS. After running My error is following
grompp error: check .molmk_martini_v2.0_surfactants.pp.log
Kindly help me I am new in this field.
I have downloaded that file again. At this time when I run program then following problem occur.It is also giving the option of default force fields of GROMACS. After running My error is following
grompp error: check .molmk_martini_v2.0_surfactants.pp.log
Kindly help me I am new in this field.
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- mnmelo
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10 years 10 months ago #1716
by mnmelo
Replied by mnmelo on topic Related to gro file of surfactant
molmaker.py tries to process your topology with grompp, but something went wrong. You'll be able to see what in the file pointed to by the error.
Manel
Manel
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- djurre
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10 years 10 months ago #1717
by djurre
Replied by djurre on topic Related to gro file of surfactant
Did you do as the message says? Check what is in (at the bottom of) .molmk_martini_v2.0_surfactants.pp.log
(note the dot in front of the file: it is a hidden file. You might not see it when you do 'ls', but it is there.)
(note the dot in front of the file: it is a hidden file. You might not see it when you do 'ls', but it is there.)
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10 years 10 months ago #1718
by mnmelo
Replied by mnmelo on topic Related to gro file of surfactant
Ah, and I'm pretty sure your problem occurs because you're not giving molmaker the martini .itp. It then looks for the default forcefields in the gromacs branch, but martini is not there. Look for the help on the -ff flag and pass it the martini_v2.*.itp file that corresponds to the martini version you're using.
Also, from what I read from your .itp name, you're using the entire surfactant itp. molmaker isn't clever enough to let you choose which molecule to generate; it'll simply take the first from the .itp file.
You'll be better off by copying the relevant molecule to a separate itp file (say, sds.itp) and work with that.
Also, from what I read from your .itp name, you're using the entire surfactant itp. molmaker isn't clever enough to let you choose which molecule to generate; it'll simply take the first from the .itp file.
You'll be better off by copying the relevant molecule to a separate itp file (say, sds.itp) and work with that.
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- satnamphysics
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10 years 10 months ago #1722
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
Thanks..I have created .gro file ..
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- satnamphysics
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10 years 10 months ago #1724
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
I have created gro file . I put 500 water and 500 sds molecules in a box . when I try to minimize it then the following error comes.
Fatal error:
Atomtype SP2 not found
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
I checked all the files. SP2 is not defined anywhere.Kindly help me.
Fatal error:
Atomtype SP2 not found
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
I checked all the files. SP2 is not defined anywhere.Kindly help me.
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- djurre
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10 years 10 months ago #1725
by djurre
Replied by djurre on topic Related to gro file of surfactant
It sounds like you are using a (very) old version of the martini_vx.x.itp file. If you download a newer one (Downloads >> Forcefield parameters >> Particle definitions) that should be fixed.
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- satnamphysics
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10 years 10 months ago #1726
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
Hi ,
At this time I have another problem during minimization. I have followed following procedure.
1) First I created a box of water and added 500 molecules of water.
2) Then I put 500 molecules SDS in that box.
3) To neutralize it I have added 500 Ions Sodium.
4) Then I mentioned number of different type of molecule in .top file and also edited martini_v2.1.itp . I pasted the topology of SDS an sodium ion in it.
5) When I run minimization then the following error occurs.
Fatal error:
number of coordinates in coordinate file (sol.gro, 3340)
does not match topology (dppc.top, 4536)
At this time I have another problem during minimization. I have followed following procedure.
1) First I created a box of water and added 500 molecules of water.
2) Then I put 500 molecules SDS in that box.
3) To neutralize it I have added 500 Ions Sodium.
4) Then I mentioned number of different type of molecule in .top file and also edited martini_v2.1.itp . I pasted the topology of SDS an sodium ion in it.
5) When I run minimization then the following error occurs.
Fatal error:
number of coordinates in coordinate file (sol.gro, 3340)
does not match topology (dppc.top, 4536)
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10 years 10 months ago #1727
by djurre
Replied by djurre on topic Related to gro file of surfactant
It's hard to help with problems like this. One of the following is wrong:
-Not all molecules have been placed in the gro file (I assume you used genbox to put them there).
-The number of beads in the .gro file is not correctly stated in the second line.
-The number of beads in one of the molecules in your top file is different from that in the gro file.
-Not all molecules have been placed in the gro file (I assume you used genbox to put them there).
-The number of beads in the .gro file is not correctly stated in the second line.
-The number of beads in one of the molecules in your top file is different from that in the gro file.
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- satnamphysics
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10 years 10 months ago #1733
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
Dear Djurre,
In the box there are three type of material. 1)dppc 128 molecule,2)Water 512 molecule,3) SDS 128 molecule. To neutralize it I have added 128 ions of sodium
I have a problem when I run simulation .Then following error comes.
Fatal error:
Invalid T coupling input: 3 groups, 2 ref_t values and 2 tau_t values
In the box there are three type of material. 1)dppc 128 molecule,2)Water 512 molecule,3) SDS 128 molecule. To neutralize it I have added 128 ions of sodium
I have a problem when I run simulation .Then following error comes.
Fatal error:
Invalid T coupling input: 3 groups, 2 ref_t values and 2 tau_t values
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10 years 10 months ago #1734
by djurre
Replied by djurre on topic Related to gro file of surfactant
This is a very different problem than the one you reported before. This time there is a mistake in you mdp file: You are specifying three groups for temperature coupling but only two temperatures/tau values.
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- satnamphysics
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10 years 10 months ago #1735
by satnamphysics
Replied by satnamphysics on topic Related to gro file of surfactant
Hi
Now how to solve this.What I have to add or remove from .mdp file
Now how to solve this.What I have to add or remove from .mdp file
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10 years 10 months ago #1736
by djurre
Replied by djurre on topic Related to gro file of surfactant
You have to add one more temperature and one more tau_t value.
This is really a very basic, non-Martini related problem. If you're not able to solve those kind of problems, you should seriously consider doing some gromacs tutorials and following a course/workshop/summerschool somewhere.
This is really a very basic, non-Martini related problem. If you're not able to solve those kind of problems, you should seriously consider doing some gromacs tutorials and following a course/workshop/summerschool somewhere.
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