[gmx-users] (no subject)

David spoel at xray.bmc.uu.se
Wed Jul 17 09:53:28 CEST 2002

On Wed, 2002-07-17 at 10:12, cathy wrote:
> Hi,
>  I would like to constraint a set of atoms coordinates to given
> positions in my protein. I have only a pdb file (or gro file) containing
> all the atoms in the wrong positions and a second file containing only
> the CA positions in the desired positions. I have tested grompp with an
> additional input pdb file as suggested in the manual but after
> minimisation the result is not correct. Is it necessary that the two
> files have the same number of atoms According to the gmx-user mailing
> list it seems true. Is there an alternative way to do what I need ?
You have to add the other atoms to your Ca pdb file. However, their
coordinates do not matter, as long as you are constraining (restraining)
only the Ca atoms. With g_confrms you could also fit the first molecule
on the second (based on Ca only) and get as output the whole first
molecule rotated and translated. It is however not clear to me whether
you want to simulate a conformational transition or just fit.

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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