[gmx-users] Re: Re: Re:Chain Terminus

Thu Jul 1 09:30:10 CEST 2010

> 
> Message: 5
> Date: Thu, 01 Jul 2010 00:13:41 +1000
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re:Chain terminus
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbe6cb2345126.4c2bddb5 at anu.edu.au>
> Content-Type: text/plain; charset="us-ascii"
> 
> 
> 
> ----- Original Message -----
> From: lloyd riggs <lloyd.riggs at gmx.ch>
> Date: Wednesday, June 30, 2010 21:55
> Subject: [gmx-users] Re:Chain terminus
> To: gmx-users at gromacs.org
> 
> > 
> > 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?  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 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...

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.

> 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.¨

Competition

Sincerely

Stephan Watkins

> 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
> gmx-users at gromacs.org
> 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