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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 1 21:23:07 CEST 2010

Hi Stephan,


> 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...

It must have been a disappointment while going for your drivers
license, that the lessons didn't involve off road racing. But it's
true: tutorials are meant for you to learn to walk. The running you'll
have to get to yourself. Are you already up to that point?

But what is actually so different about your system that makes it
difficult to deal with using a standard (tutorial-like) protocol?
Okay, the system is big, but that shouldn't be an issue. The sequence
is the same (http://www.nmr.chem.uu.nl/~tsjerk/course/molmod/01-Preparation-Workflow.jpg),
starting with generating topologies for your chains. In some cases,
especially if building a topology for a chain requires some special
attention, like setting protonation states or termini, it may be
convenient to first split the structure into separate files,
processing each separately to construct a topology. Going the opposite
way, adding all pieces together, including solvent and ions and such,
and then trying to get a complete topology for the whole lot in one go
with pdb2gmx may easily get you in trouble.

> I have a smart question though, why do computer folks have an insssesant need to be correct, or smart, or image based things?

Correct and smart is not by need, but just the way it is :p But an
incessant need to be image based things?

Hope it helps,

Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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