[gmx-users] Making covalent bonds between protein subunits

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 25 12:15:30 CEST 2001

On Thu, 25 Oct 2001, K.A.Feenstra wrote:

>> an alternative solution: Instead of specifying new covalent bonds, you could define *distance restraints* on the calcium and monomer atoms (see
>> GROMACS manual). These are, roughly speaking, also harmonic potentials. Maybe they work better.
>Two remarks:
>1) depending on the parameters, distance restraints can be exactly harmonic potentials.
>2) bonds usually are *not* represented by harmonic potentials, but by constraints
>   (don't confuse constraint and restraint, a constraint is a fixed distance w/o potential).
>But, I would think Volkers' suggestion is a good one (let's hope it works).
I'm afraid not, the distance restraints still have to be within the
molecule in GROMACS definition.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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