[gmx-users] pseudo atoms

sadhna sadhana at che.iitb.ac.in
Wed Oct 31 18:36:13 CET 2001

    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.

On Wed, 31 Oct 2001, David van der Spoel wrote:

> On Wed, 31 Oct 2001, sadhna wrote:
> >
> >hi,
> >    my input pdb file contains hydrogen as well as pseudoatoms.
> >Since gromacs is not able to recognize pseudoatoms how should i ignore
> >pseudoatoms in the pdb file.
> What kind of pseudo atoms? If you e.g. have TIP4P water you need to retain
> the M position, so you can not use pdb2gmx. Other programs will however
> read pdb files as well, so maybe you don't need pdb2gmx at all.
> 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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