[gmx-users] Re:Chain terminus

lloyd riggs lloyd.riggs at gmx.ch
Wed Jun 30 13:55:21 CEST 2010

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 .gro output still has no chain ID's, and there is a change in the number/type of atoms so a new .top has to be generated.  If I use either of the new .gro or .pdb files, 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?

Also, I probably would have not figured this out so fast without the replies I had, mostly.

Mit freundlichen Grüsse

Stephan Watkins
GMX DSL: Internet-, Telefon- und Handy-Flat ab 19,99 EUR/mtl.  
Bis zu 150 EUR Startguthaben inklusive! http://portal.gmx.net/de/go/dsl

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