Help To Extract 1 Frame from Mapped Traj

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yipy0005
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9 years 9 months ago #3969 by yipy0005

Help To Extract 1 Frame from Mapped Traj was created by yipy0005

Hi, I was following the martini tutorial on parameterizing new molecules. However, at the step when I'm supposed to extract one frame from the mapped.xtc, I realised I don't have a CG-ed ligand.gro to read my mapped.xtc. Therefore, what can I do?

Thanks, any help would be greatly appreciated.

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Clement
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9 years 9 months ago #3970 by Clement

Replied by Clement on topic Help To Extract 1 Frame from Mapped Traj

You created your mapped.xtc with trjconv and an index file? Then output the frame a t = 0 (play with the -b and -e flags) as a .gro file.

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yipy0005
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9 years 9 months ago #3971 by yipy0005

Replied by yipy0005 on topic Help To Extract 1 Frame from Mapped Traj

Yup, but the -f flag requires an input file, which I don't think was generated.

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Clement
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9 years 9 months ago #3972 by Clement

Replied by Clement on topic Help To Extract 1 Frame from Mapped Traj

If you obtained a mapped.xtc file using g_traj, then you can just rerun the same command line and extract the first frame by adding -e 0 -o first-frame.gro.

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yipy0005
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9 years 9 months ago #3975 by yipy0005

Replied by yipy0005 on topic Help To Extract 1 Frame from Mapped Traj

Thanks, that works totally.! From the tutorial where we solvate ubiquitin with CG water, now I wish to solvate my protein in CG octanol. Where can I find the .gro files for the CG octanol? =)

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Clement
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9 years 9 months ago #3976 by Clement

Replied by Clement on topic Help To Extract 1 Frame from Mapped Traj

Mmmmh... Not available on our website. You just have to build it yourself! Two beads, shouldn't be too hard. You can probably change your topology file and minimize your water into octanol...

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yipy0005
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9 years 9 months ago #3977 by yipy0005

Replied by yipy0005 on topic Help To Extract 1 Frame from Mapped Traj

Lol, I'm already doing that currently, Just wanna make sure we are not using too much time when there's a ready-made file if any. So, u mean I parameterize my octanol by solvating it as a ligand in water.? =)

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Clement
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9 years 9 months ago #3982 by Clement

Replied by Clement on topic Help To Extract 1 Frame from Mapped Traj

Octanol is already parameterized... See here: md.chem.rug.nl/cgmartini/images/paramete...ni_v2.0_solvents.itp . What I meant is Martini is probably flexible enough to find a way to build octanol from random water beads. What is your current system topology (.top)?

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yipy0005
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9 years 9 months ago #3983 by yipy0005

Replied by yipy0005 on topic Help To Extract 1 Frame from Mapped Traj

Yup, instead of building octanol from random water beads, I built it from the AA octanol solvent topology from GROMACS. It works well so far. =)

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Clement
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9 years 9 months ago #3984 by Clement

Replied by Clement on topic Help To Extract 1 Frame from Mapped Traj

yipy0005 wrote: I built it from the AA octanol solvent topology from GROMACS.

I sincerely have no clue what you're doing... Sounds way more complicated than it would need to be.

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