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!
Mark
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