[gmx-users] pseudo atoms

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 31 19:29:08 CET 2001

On Wed, 31 Oct 2001, sadhna wrote:

>    The pdb file has been created by program DYANA. In DYANA for
>calculating proton distance for eg in leucine they have created a
>pseudoatom at the center of two delta methyl groups of leucine
>and calculated distances with respect to that pseudoatom. Similarly
>pseudoatoms have been created for AIB and other residues.
and do you want to do something similar in gromacs, i.e. nmr refinement,
or will it be unrestrained MD? Usually the NMR particles are called M*
so it shouldn't be too hard to filter them out using grep.
pdb2gmx will add the real hydrogen positions for you.

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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