----- Original Message ----- From: lloyd riggs <[email protected]> Date: Thursday, July 1, 2010 17:31 Subject: [gmx-users] Re: Re: Re:Chain Terminus To: [email protected]
> > > > > Message: 5 > > Date: Thu, 01 Jul 2010 00:13:41 +1000 > > From: Mark Abraham <[email protected]> > > Subject: Re: [gmx-users] Re:Chain terminus > > To: Discussion list for GROMACS users <[email protected]> > > Message-ID: <[email protected]> > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > ----- Original Message ----- > > From: lloyd riggs <[email protected]> > > Date: Wednesday, June 30, 2010 21:55 > > Subject: [gmx-users] Re:Chain terminus > > To: [email protected] > > > > > > > > Dear All, > > > > > > I had posted here a week or so ago, but fixed my problem, > and > > > wanted to post it, and ask if somone has a better method for this: > > > > > > Basically, I have 5 different proteins A-E in a pdb file. > > > > > > I can generate a toplogy initially with pdb2gmx automated, > which > > > places the NH3 and COO- terminus. > > > > > > The resulting .gro file looses the chain ID's. This > > > initial .gro and .top file works for runs (MD or EM). > > > > > > I then add a box and waters, and the genbox has a built in > code > > > for changing the .top file to match the water, which also > keeps > > > the terminal ends properly. These files work for runs > (MD > > > and EM) > > > > > > Now, then I add Ions (Na, K, Mg, Ca, Cl). The .top > file > > > however is not updated with genion. The resulting .pdb > or > > > > genion -p should do all this for you. I imagine decent > tutorial material > > points this out... > > > > > .gro output still has no chain ID's, and there is a change > in > > > > Correct, because GROMACS doesn't care about them because it > makes no > > post-pdb2gmx use of them. > > > > > the number/type of atoms so a new .top has to be > > > generated. If I use either of the new .gro or .pdb files, > > > > No, you only need a modified .top. It's straightforward to > make sure that > > you have #include "ions.itp" and then to edit the [molecules] > section.> Compare your before-and-after .top files with the diff > tool to see what I mean. > > > > > the terminal ends are not maintained, nor can pdb2gmx > recognize > > > the terminus in the interactive session without chain IDS, > and > > > the resulting .top files leed to MD and EM runs crashing, or > not > > > even initiallizing. > > > > > > To get around this, I write out a .pdb, cut and paste the > > > protein portion only and add back the chain IDs, which > allows > > > interactive assignment of the terminuses. This is > however > > > time consuming, as it has to be done each time for each ion. > > > > > > I woundered if anyone knows how to do this more > efficienttly, > > > like the genbox or anothe way? > > > > genion -p or a few minutes with your .top file and a text editor > > post-genion would have sufficed. > > > > > Also, I probably would have not figured this out so fast > without > > > the replies I had, mostly. > > > > > If you'd told us the problem was in producing a post-genion > .top, then you > > might have been told about genion -p straight away. I don't > think I ever > > understood why (you thought) you needed chain IDs - that could > have been my > > oversight, but I certainly wasn't motivated to delve into your > mind to find > > out why you wanted them. This is a good lesson in not > presupposing the > > form of the answer to a problem when asking for help :-) > Describe the real > > > > problem, not only your secondary problems with your solution > approach. The > > "How to ask questions the smart way" website makes this advice too! > > > > (You mean with a hose and some duck tape?) > > Genion P doesn't work for me without a text editing session, so > is basically the same. Probably I do something wrong? Sounds like it. > Theres differences in the atoms after, complaints in numbers, > etc... The Terminus in the internal chains loose atoms (ie > Hydrogens for NH3 and COO-, which either have to be replaced Sounds like you're mismatching files from different stages of the system preparation. Doing each stage in a separate directory is a good way to avoid doing that. > after genion with a text editor, or just re added with something > like "PDB editor", a nice freeware tool I found. The chain > ID addition with PDB editor works faster, but the editor has > problems with larger files than 1-2 MB. > > > No, you only need a modified .top. It's straightforward to > make sure that > > you have #include "ions.itp" and then to edit the [molecules] > section.> Compare your before-and-after .top files with the diff > tool to see what I >mean. > > I did this from the biggening, it's strait forward as you > said. The problems with the tutorials is they already > work, and are missing a shlew of problems one may incounter when > doing more complicated things, etc... Yup, that's the nature of the beast, in research. > I was doing this, comparing before and after files, most of the > text editors for comparing two files though will not open a 37 > megabyte file, let alone two for a simple comparisson. > Even Emacs has a problem. I basically only got number of > atoms 1 and atoms 2. The file editing I was suggesting was of the .top file. You should never need to edit a post-genion coordinate file, and if you need to look at or search one, use "less", rather than an editor that needs to load the whole file. > > problem, not only your secondary problems with your solution > approach. The > > "How to ask questions the smart way" website makes this advice too! > > > > > I have a smart question though, why do computer folks have an > insssesant need to be correct, or smart, or image based > things? Just kidding. It's hard to ask a question > when you have to look through 500,000 atoms and find the ten > that are missing, unless you know what to look for first. > I had assumed it was this, the terminal atoms. It does > make it a little difficult though as when adding Ions, there are > also another 400-500 atoms changed, and waters lost, etc....so > it looks like something worse is going on from somone whom > hasn't used gromacs much.(oh my god is blowing up) > > In the end though, both methods seem to be about the same in > time aspect. I also found you can run genion 3-5 times for > the varied ion additions, and then do one final text editing to > add the chain ID's, and use pdb2gmx only once to make the final > .top file. > > Thank you for the advice.¨ No worries. I still think your problem should have a trivial solution... Mark > > Mark > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > http://lists.gromacs.org/pipermail/gmx- > users/attachments/20100701/6c2e7dde/attachment.html> > > ------------------------------ > > > > -- > > gmx-users mailing list > > [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search > before posting! > > > > End of gmx-users Digest, Vol 74, Issue 186 > > ****************************************** > > -- > GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern > E-Mail & mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? 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