[gmx-users] pseudo atoms

[David van der Spoel]

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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