normal Parametrizing a new molecule based on known fragments

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3 months 3 days ago #7295 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Dear Pim,

Thanks for your answer.

If I want to consider C5-CO-AAVVLLWEE and C10-CO-AAVVLLWEE, are they sensible?

Best,
Leila

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3 months 3 days ago #7296 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
Well, I suppose they would make 7:2 and 12:3 mappings, that's fine too. Just remember that you wouldn't really be able to distinguish between C5, C6 and C7, or C9/C10/C11 as they would have the same mapping, unless you start working with Small beads, and I don't really recommend that for this case.

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3 months 2 days ago #7297 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Dear Pim,
Thanks for quick reply.

I have a question about C15-CO part of C15-CO-AAVVLLWEE.

Your suggestion about C15-CO-AAVVLLWEE was as follows.

"I would map the aliphatic part to four beads as it's 17 heavy atoms. The first 12 carbons should be 3 C1 particles, the C-C-C-CO- you can debate about, maybe it can be Na."

There is another possibility:
C-C-C-C-C, C-C-C-C, C-C-C-C-, C-C-C-O

What is difference between your suggestion and my case (another possibility)?

Which of them is appropriate for CG mapping.

Best,
Leila

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3 months 2 days ago #7298 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
You could argue that 'my' mapping is slightly more appropriate: we have a rule of thumb that if you have to make 1 bead larger it's generally better to take the most branched group of atoms, as they are more spherical and occupy less volume. As the O of your structure is out of the chain, that makes more sense. However, the difference is (hopefully) not crucial.

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1 month 2 weeks ago #7355 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Hi all,

I am doing CG MD simulation (self-assembly of peptide amphiphile). I viewed trajectory file. I have pbc problem:

ln.sync.com/dl/f9182b590/2eejeayz-54nxm996-t2iu8fn2-mg8i7htv

I used the following commands:

gmx_mpi trjconv -f a.xtc -s a.tpr -n index.ndx -o nojump.xtc -pbc nojump

gmx_mpi trjconv -f nojump.xtc -s a.tpr -n index.ndx -o new.xtc -pbc mol -center

But pbc problem was not solved.

ln.sync.com/dl/e48ff49a0/2cj5tgh7-cy9azz2x-2a9nr9n5-fmftabsv

Is my manner true?

How to resolve this issue?

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1 month 2 weeks ago #7356 by riccardo
riccardo replied the topic: Parametrizing a new molecule based on known fragments
You probably want to do this:

gmx_mpi trjconv -f a.xtc -s a.tpr -n index.ndx -o whole.xtc -pbc whole

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1 month 2 weeks ago #7357 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Dear Ricardo,

Thanks for your answer.

After using -pbc whole, the problem was not solved:

ln.sync.com/dl/3fcb57130/e6d5ki2j-jwgs2pai-pe6c55zk-huzt2y33

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1 month 2 weeks ago #7359 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
The approaches that you and Riccardo took don't do what you want, because you have many small molecules. It makes all molecules whole, but still half of them are on the 'left' and half on the 'right'. To be honest, I wouldn't call it a problem. It is also not so trivial to solve because you have multiple clusters: if you translate your big cluster to be whole, perhaps you will cut another one across the periodic boundaries. -pbc whole usually works less well than -pbc mol by the way.

If you want a better visualization, you can use VMD to display the adjacent simulation box image (Periodic menu in Graphical Representations). If you really need to have your big cluster in the center of your box, you could use -pbc mol first and then -pbc cluster, or isolate it with gmx clustsize and use editconf -princ (tips on this procedure are in the analysis section of the self-assembly tutorial, cgmartini.nl/index.php/tutorials-general...eptide-gmx5#Analysis )

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1 month 2 weeks ago #7360 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Dear Pim,

Thanks for your answer.

*** I tried the Periodic menu in Graphical Representations in VMD. It was good.

*** I used -pbc mol first and then -pbc cluster -center. I have a better visualization, now.

*** The link you suggested about the analysis section of the self-assembly tutorial, I encountered with " you are not authorised to view this resource ". Why???
I have another question. There are 10 aminoacids in my structure. I want to see them with bonds using the cg_bonds.tcl in trajectory file using vmd.

source cg_bonds.tcl

After using the following commands:

cg-bonds -top *.top -topoltype martini

I encountered with:

atomsel: setbonds: Need one bondlist for each selected atom

==============================================================

after using following commands:

cg-bonds -tpr *.tpr -topoltype martini

I encountered with:

couldn't write file "/dev/null": no such file or directory

How to resolve that?

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1 month 2 weeks ago #7361 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
Sorry, the tutorial is under construction and access is restricted until the end of the month. There is a gmx 4 version in the tutorial section ( cgmartini.nl/index.php/tutorials-general...-ht-peptide#Analysis ), but it was a bit different compared to gmx 5. Anyway you solved the problem already.

For CG_bonds, you have to specify all flags at the same time, so cg_bonds -tpr *.tpr -top *.top -topoltype martini -gmx /path-to/gmxdumpscript

For Gromacs 5, unfortunately gmx dump is not the same as previous gmxdump.
You will need a script somewhere that you can refer to in the above command. The script is very simple and as follows:

#!/bin/bash

source /usr/local/gromacs-2016.1/bin/GMXRC

gmx dump $@

And then of course you have to change the "source" line to where your version of gromacs is stored. I'm not sure it will work 100% even if you do everything correctly, so do not despair if not.

Hopefully at the end of the month we will have tutorials for both the analysis and the visualisation online for GMX 5, but hopefully you can use the above until then.

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1 month 1 week ago #7362 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Dear Pim,
Thanks for your answer.

I did every things you said step by step for gmx 5. But problem was not solved.

I transferred my files to the linux system with Rocks OS and gromacs 4.5.4.

According to the example in cg_bond.tcl file, I used following command in TkConsole of VMD:

cg_bonds -tpr *.tpr -top *.top -topoltype martini -gmx /opt/bio/gromacs/bin/gmxdump

But again I encountered with:

atomsel: setbonds: Need one bondlist for each selected atom

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1 month 1 week ago #7363 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
Perhaps your .tpr and/or .top do not contain exactly the same amount of molecules as the .gro or .xtc? Did you for example remove the waters in the coordinates? The script is not very robust, unfortunately. Otherwise, I also don't know why it wouldn't work. The script works for me on short peptides, even with only flags -gmx and -tpr, without -top and -topoltype.

Pim

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1 month 1 week ago #7364 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
You guess truely. I had removed waters.

I get a new.tpr file using gmx_mpi convert-tpr containing only solute.

After using the following command:

cg_bonds -tpr new.tpr -topoltype martini -gmx /opt/bio/gromacs/bin/gmxdump

I encountered with:

child process exited abnormally

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1 month 1 week ago #7365 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
2 questions:

1. Can you try on the trajectory with water molecules instead of the trajectory without water and the converted tpr?
2. Which version of gmx did you use for the simulations? Which version of gmxdump are you now calling?

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1 month 1 week ago #7366 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Answers:

1. My systems is very large (40 GB). Trying trajectory with water is hard for me. I will try that.

In fact for simulation, I used a cluster that I access it by remote.

For viewing the trajectory directly in vmd in linux, I used another system. Thus, I use trajectory file without waters. Transferring the trajectory with waters from the cluster to my system is hard and time consuming.

2. The version of gmx did I use for the simulations is 5.1.3

The version of gmxdump I now calling is 4.5.4

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1 month 1 week ago #7367 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
So yeah, you can't mix gmx4 and gmx5 files like that.
If you specify both tpr and top you usually don't need the gmxdump. So the last thing you can try is cg_bonds -tpr topol.tpr -top topol.top without -gmx

Otherwise, you have to compile gromacs 5 somewhere and then use the script I gave yesterday to link gmxdump to the correct gromacs 5 version.

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1 month 1 week ago #7368 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
Also, you don't need the whole trajectory loaded, the last frames or only some intermediate frames should also work.

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1 month 6 days ago #7370 by l_karami
l_karami replied the topic: Parametrizing a new molecule based on known fragments
Dear Pim,

I used trajectory with water molecules and only cg_bonds -tpr topol.tpr -top topol.top in VMD. My problem was solved. Thanks for your step by step guidance.

My system is CH3-(CH2)15-CO-AAVVLLLWEE. I want to see peptide part (AAVVLLLWEE) of the last frame of CG MD simulation using the cg_bonds in VMD.

For one peptide, in my system:

ln.sync.com/dl/3d9367d00/3axb6ct5-vi7g53z9-criuhpce-h8vf23z6

I want to have my peptide same as the figure in some papers (yellow circle):

ln.sync.com/dl/4d471dc30/qac9mir8-gur5m8xy-xs5iu7gs-f242rjac

How to obtain that?

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1 month 6 days ago #7371 by Pim
Pim replied the topic: Parametrizing a new molecule based on known fragments
Hey, that's a little less straightforward. There is a rudimentary tool available on cgmartini.nl/index.php/tools2/visualization
If you download cg_secondary_structure.tcl and the POSIX LA package described there, you can draw some (basic) beta sheet ribbons.
I don't know how the people in your paper did it, maybe with backmapping?

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