[gmx-users] incorporating itp files

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 27 22:50:23 CET 2002

On Wed, 27 Mar 2002, Senthil Kandasamy wrote:

>I want to practice running some simulations using GROMCACS before I jump 
>into my specific system.
>So I downloaded some pdb files from Peter Tielemen's  web site. I chose the 
>dppc64.pdb file.
>The first order of business is to generate a .gro file, I guess.
>So I typed pdb2gmx -f dppc64.pdb using forcefield option 0.

pdb2gmx is only for proteins.
You can just use the pdb file as is (or convert it to gro with editconf).
Use the itp file by manually creating a top file around it (see printed
manual for the format).

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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