Tsjerk,
I can only describe the project in a private communication, as this is a
completely new idea (potentially high-risk from the experimental
standpoint) in a very competitive field. If you're interested, please let
me know, and I'll email you directly. Other than that, there is not much I
can
Hi Alex,
I've done it before, but I can't do it from the top of my head without
seeing the input and checking what Gromacs wants. It's not hard work, it's
not a lot of work, but it is work, and more than we'll usually consider
doing for answering a post on the mailing list. On the other hand, you
Hi Tsjerk,
You're right. It's just that the last time I used a sed or awk script of my own composition was in college, which is ~13 years ago. :))
So, this is still an undertaking for someone like me. But yes, what you said is well taken. Lack of knowledge/desire to rename atoms in text files
Hi Alex,
Writing a sed oneliner is not the same as writing a renaming script. I
commonly use them to process PDB files in some way and it's surprising how
much you can do without scripting.
Cheers,
Tsjerk
On Apr 3, 2015 7:13 PM, "Alex" wrote:
> Gentlemen,
>
>
> Building a script to rename the
Mauricio,
That is very useful, thanks a lot. I'll try it in a bit.
Alex
MEN> Alex,
MEN> You can use X3DNA to produce any nucleic acid geometry you’d like and
MEN> gromacs pdb2gmx will understand it.
MEN> For example, to create a single-strand of 16 DNA bases you only need a file
MEN> with th
Gentlemen,
Building a script to rename the atom is obviously an option. I was just wondering if I missed something, e.g. a VMD plugin that could do it quickly. As far as google searching, I have done that, and I have found some things (like the make-NA server, or this: http://smog-server.org/c
Alex,
You can use X3DNA to produce any nucleic acid geometry you’d like and
gromacs pdb2gmx will understand it.
For example, to create a single-strand of 16 DNA bases you only need a file
with the corresponding rigid-body base-step parameters such as the
ssdna.par file shown below:
16 # bases
On 03/04/2015 5:53 pm, "Mark Abraham" wrote:
>
> Hi,
>
> I tried that search myself and found some things that looked potentially
useful to you, so I suggested that search. Either you might find something
useful there, or the dialogue could progress about what you need. Requiring
perfect input for
Hi,
I tried that search myself and found some things that looked potentially
useful to you, so I suggested that search. Either you might find something
useful there, or the dialogue could progress about what you need. Requiring
perfect input for pdb2gmx is a fairly stringent expectation.
Mark
On
Hi Alex,
You've solved the issue of getting a DNA structure, but now you're facing a
problem of getting Gromacs to prune it. That has to do with the naming
scheme mainly. Your best bet is using sed to do name substitution. Probably
google will give some good hints about such substitutions in PDB f
Mark,
Not to troll, but why did you assume that I didn't do my due diligence before posting here?
Because, you see, you could have left that second part of your reply (which only confirms the legitimacy of my initial question), and it would make it less insulting.
Alex
>
Hi,
Googling
Hi,
Googling things like "gromacs DNA structure" is a good bet. There are no
fully standardised naming schemes or workflows, so you will likely not have
something do everything for you.
Mark
On 03/04/2015 7:03 am, "Alex" wrote:
> I'm fully aware that this is a forum for discussing Gromacs, but
I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it.
I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything
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