[gmx-users] Re:Chain terminus

Mark Abraham mark.abraham at anu.edu.au
Wed Jun 30 16:13:41 CEST 2010

----- 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!


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