[gmx-users] pseudo atoms

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 31 14:09:28 CET 2001

On Wed, 31 Oct 2001, sadhna wrote:

>    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

More information about the gromacs.org_gmx-users mailing list