[gmx-users] fatal error, working with dimeric protein

[David van der Spoel]

On Tue, 11 Dec 2001, Geraudis Mustelier wrote:

>I would like to apply the energy minimization to a dimeric protein molecule.
>These chains (A and B), belong to the same molecule, must not be treated
>independently. I would like restrain or fix all atoms except those that
>belong to one residue range in the chain A.
>In the pdb file generated with pdb2mgx the atoms are numbered in continuum
>form, but, appear two topology files, one for each chain. These topology
>files starts with number one. In contrast, make_ndx and genpr work with the
>pdb file in continuum numeration, so, I obtain the following errors running
>grompp.
You have the position restraints in the wrong place. Since pdb2gmx
generates them for you, for each chain individually, the easiest is to
edit your posre_A.itp manually, and remove the atom numbers referring to
the residue you want unrestrained. The turn on the position restrains in
your mdp file using define = -DPOSRES

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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