Re: [gmx-users] GMX-compatible DNA coordinates

[Alex]

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" <nedoma...@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.abra...@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" <nedoma...@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" <nedoma...@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 >> >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >> >> >> >> >> >> --  >> >> Best regards, >> >>  Alex                            mailto:nedoma...@gmail.com >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. --  Best regards,  Alex                            mailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.

-- 

Best regards,

 Alex                            mailto:nedoma...@gmail.com

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