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

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 12 09:33:24 CET 2001

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
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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