[gmx-users] GMX-compatible DNA coordinates

Fri Apr 3 21:33:05 CEST 2015

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 can
always try to raise interest in a collaboration, which is a completely
different matter :)

Cheers,

Tsjerk

On Fri, Apr 3, 2015 at 8:21 PM, Alex <nedomacho at gmail.com> wrote:

>  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
> shouldn't hinder research.
>
> I do think that having a person such as yourself of Justin on my team to
> implement what I have in mind would speed things up tremendously, but noone
> seems to be interested, hint-hint. ;)
>
>
> Thanks,
>
>
> Alex
>
>
>
>   >
>
> 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" <nedomacho at gmail.com> wrote:
>
>
> 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/cgi-bin/GenTopGro.pl). This is still not quite
> what I was aiming for. Hence, my initial question. I didn't mean to be
> snippy, but I did try searching, believe me. On the other hand, I assume
> that you are much better versed in the problem at hand, so then maybe you'd
> be able to appreciate info I simply ignored. Obviously, I welcome anything
> you can suggest. If this boils down to me writing a renaming script, so be
> it. :)
>
>
> Thanks,
>
>
> Alex
>
>
>
>   >
>
>
> On 03/04/2015 5:53 pm, "Mark Abraham" <mark.j.abraham at gmail.com> 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 pdb2gmx is a fairly stringent expectation.
>
> i.e. The use of sed or similar tools is normal, as Tsjerk says also. There
> are too many options, and nobody has built the Babel fish of MD input!
>
> Mark
>
> > Mark
>
> >
>
> > On 03/04/2015 3:40 pm, "Alex" <nedomacho at gmail.com> wrote:
>
> >>
>
> >> 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 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" <nedomacho at gmail.com> wrote:
>
> >>
>
> >>
>
> >> 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 as is. You suggested AMBER in the past, so
> AMBER it is.
>
> >>
>
> >>
>
> >> ChemOffice produced a PDB with incompatible atom types. make-na server (
> http://structure.usc.edu/make-na/server.html) also produced something
> pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
> usable topology out of the box with an established potential implemented in
> Gromacs? Anything that will not involve manual modification of PDBs or
> writing text-processing scripts will make me very happy.
>
> >>
>
> >>
>
> >> I will really appreciate any suggestions.
>
> >>
>
> >>
>
> >> Thank you,
>
> >>
>
> >>
>
> >> Alex
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> --
>
> >>
>
> >> Gromacs Users mailing list
>
> >>
>
> >>
>
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>
> >>
>
> >>
>
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>
> >>
>
> >>
>
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> >>
>
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>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> --
>
> >>
>
> >> Best regards,
>
> >>
>
> >>  Alex                            mailto:nedomacho at gmail.com
>
> >>
>
> >>
>
> >> --
>
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>
> >>
>
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>
> >>
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>
>
>
>
> --
>
> Best regards,
>
>  Alex                            mailto:nedomacho at gmail.com
> <nedomacho at gmail.com>
>
>
> --
>
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> --
>
> Best regards,
>
>  Alex                            mailto:nedomacho at gmail.com
> <nedomacho at gmail.com>
>
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.