[gmx-users] splitting chains

Mark Abraham Mark.Abraham at anu.edu.au
Sat Mar 31 06:06:50 CEST 2007

Tsjerk Wassenaar wrote:
> Ozge,
> We are, at least I am, getting the impression that you refuse to try
> to think for your self. This makes trying to help you very
> unsatisfactory. We are not here to do your homework.
> Ok, that been said, I'll make it brief. You shouldn't need to edit the
> specbond.dat (in the gromacs topology/data directory). Issuing -merge
> with pdb2gmx will make it recognize multiple chains as one molecule
> allowing interchain bonds.
> Next time, please be more prepared, at least suggesting that you've
> tried some things (reading?) to find a solution to your problem and
> give more thoughts about phrasing your question (english, logic,
> information required).

To be fair, the manual doesn't mention specbond.dat, which is one of the 
more glaring errors, IMO. Searching the mailing list archives will give 
some instruction though, and Ozge should have tried this.

I hope there's also been a serious effort to read chapter 5 of the 
manual, since this sort of topology-tweaking is ludicrous to attempt 
without that. Then again, I've seen lots of people attempt ludicrously 
inappropriate things, and not all of them have been with MD!


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