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<p>Hi Tsjerk,</p>
<p><br></p>
<p>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. :))</p>
<p>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.</p>
<p>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. ;)</p>
<p><br></p>
<p>Thanks,</p>
<p>
<br>Alex</p>
<p><br></p>
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<p><span class=rvts7>Hi Alex,</span></p>
<p><span class=rvts7>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.</span></p>
<p><span class=rvts7>Cheers,</span></p>
<p><span class=rvts7>Tsjerk</span></p>
<p><span class=rvts7>On Apr 3, 2015 7:13 PM, "Alex" <</span><a class=rvts8 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts7>> wrote:</span></p>
<p><br></p>
<p><span class=rvts7>Gentlemen,</span></p>
<p><br></p>
<p><span class=rvts7>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: </span><a class=rvts8 href="http://smog-server.org/cgi-bin/GenTopGro.pl).">http://smog-server.org/cgi-bin/GenTopGro.pl).</a><span class=rvts7> 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. :)</span></p>
<p><br></p>
<p><span class=rvts7>Thanks,</span></p>
<p><br></p>
<p><span class=rvts7>Alex</span></p>
<p><br></p>
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<p><span class=rvts7>On 03/04/2015 5:53 pm, "Mark Abraham" <</span><a class=rvts8 href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a><span class=rvts7>> wrote:</span></p>
<p><span class=rvts7>></span></p>
<p><span class=rvts7>> Hi,</span></p>
<p><span class=rvts7>></span></p>
<p><span class=rvts7>> 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.</span></p>
<p><span class=rvts7>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! </span></p>
<p><span class=rvts7>Mark</span></p>
<p><span class=rvts7>> Mark</span></p>
<p><span class=rvts7>></span></p>
<p><span class=rvts7>> On 03/04/2015 3:40 pm, "Alex" <</span><a class=rvts8 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts7>> wrote:</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Mark,</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Not to troll, but why did you assume that I didn't do my due diligence before posting here? </span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> 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.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Alex</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> ></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Hi,</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> 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.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Mark</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> On 03/04/2015 7:03 am, "Alex" <</span><a class=rvts8 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts7>> wrote:</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> 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.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> 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.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> ChemOffice produced a PDB with incompatible atom types. make-na server (</span><a class=rvts8 href="http://structure.usc.edu/make-na/server.html">http://structure.usc.edu/make-na/server.html</a><span class=rvts7>) 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.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> I will really appreciate any suggestions.</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Thank you,</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Alex</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> --</span></p>
<p><span class=rvts7>>></span></p>
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<p><span class=rvts7>>> </span><a class=rvts8 href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users</a><span class=rvts7> or send a mail to </span><a class=rvts8 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><span class=rvts7>.</span></p>
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<p><span class=rvts7>>> -- </span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Best regards,</span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> Alex mailto:</span><a class=rvts8 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>></span></p>
<p><span class=rvts7>>> --</span></p>
<p><span class=rvts7>>> Gromacs Users mailing list</span></p>
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<p><span class=rvts7>-- </span></p>
<p><span class=rvts7>Best regards,</span></p>
<p><span class=rvts7> Alex </span><a class=rvts8 href="mailto:nedomacho@gmail.com">mailto:nedomacho@gmail.com</a></p>
<p><br></p>
<p><span class=rvts7>--</span></p>
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<p><span class=rvts9>-- </span></p>
<p><span class=rvts9>Best regards,</span></p>
<p><span class=rvts9> Alex </span><a class=rvts10 href="mailto:nedomacho@gmail.com">mailto:nedomacho@gmail.com</a></p>
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