[gmx-users] GMX-compatible DNA coordinates

Alex nedomacho at gmail.com
Fri Apr 3 21:37:03 CEST 2015 

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 reveal on a public forum. I hope you'll understand. ;)

Alex


On Fri, Apr 3, 2015 at 1:33 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> --
>>
>> >>
>>
>> >> Best regards,
>>
>> >>
>>
>> >>  Alex                            mailto:nedomacho at gmail.com
>>
>> >>
>>
>> >>
>>
>> >> --
>>
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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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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>

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