[gmx-users] Re: Re: Re:Chain Terminus
Mark Abraham
mark.abraham at anu.edu.au
Thu Jul 1 11:14:52 CEST 2010
----- Original Message -----
From: lloyd riggs <lloyd.riggs at gmx.ch>
Date: Thursday, July 1, 2010 17:31
Subject: [gmx-users] Re: Re: Re:Chain Terminus
To: gmx-users at gromacs.org
>
> >
> > 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?
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
> >
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