normal top2psf.pl problem: trying to use vmd for MARTINI protein

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13 years 1 month ago #556 by johnny
Hello,

While trying to visualize a trajectory in VMD, I came across the script top2psf.pl. Has anyone had any luck with this? I am trying to simulate a protein and would like to view the corresponding trajectory.

i use it as:

> ./top2psf.pl -i martini.top -o martini.psf
this generates the error:
> Cannot open atoms for reading: No such file or directory

Anyone encounter this or have a better suggestion for getting the correct MARTINI protein information to VMD? Thank you for any help.

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13 years 1 month ago #561 by xavier

johnny wrote: Hello,

While trying to visualize a trajectory in VMD, I came across the script top2psf.pl. Has anyone had any luck with this? I am trying to simulate a protein and would like to view the corresponding trajectory.

i use it as:

> ./top2psf.pl -i martini.top -o martini.psf
this generates the error:
> Cannot open atoms for reading: No such file or directory

Anyone encounter this or have a better suggestion for getting the correct MARTINI protein information to VMD? Thank you for any help.


Do not know this script! Where did you get it?

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13 years 1 month ago #588 by johnny
available at:

www.gromacs.org/Developer_Zone/Programming_Guide/VMD

i know it is not one of your group's scripts, but i was wondering if other martini users had a similar experience. what is your preferred visualization method? thanks!

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13 years 1 month ago #589 by xavier

johnny wrote: available at:

www.gromacs.org/Developer_Zone/Programming_Guide/VMD

i know it is not one of your group's scripts, but i was wondering if other martini users had a similar experience. what is your preferred visualization method? thanks!


I personally use VMD.

That script probably works for atomistic systems but likely not for CG.

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13 years 1 month ago #593 by johnny
actually the script is ONLY for MARTINI molecules. the problem was that it says a MARTINI .top file is needed for the input, but what it actually needs is the protein's .itp file.

what do you use to adjust vmd to display MARTINI molecules?

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13 years 1 month ago #595 by xavier

johnny wrote: actually the script is ONLY for MARTINI molecules. the problem was that it says a MARTINI .top file is needed for the input, but what it actually needs is the protein's .itp file.

what do you use to adjust vmd to display MARTINI molecules?

we have an in house script that reads the tpr file and define the bonds as they should be ... then is becomes easier to play with the renderings.
the script will be soon available on the site :))

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13 years 1 month ago #596 by johnny
great! looking forward to it. you and your colleagues have been quite intellectually generous to put it mildly. thank you again.

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13 years 2 weeks ago #621 by sdf
Any progress on this? Or should I start coding?

I also tried to top2psf.pl and noticed several problems. For one, I dont think it recognizes comments beginning with ; also, it seems like it requires a dihedral statement to be there, even if there arent any dihedrals defined. Futhermore, i think the script only handles one residue per file and if it finds several, then it screws things up. Im not sure about all of these but its enough to make recoding from scratch worth the effort.

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13 years 1 week ago #622 by xavier
It is coming ....

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