[gmx-users] coordinates, topology and PRODRG
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 21 20:05:50 CET 2001
On Wed, 21 Nov 2001, Lars Poulsen wrote:
>Are there any other tools out there for converting pdb coordinates to gromacs coordinates and creating topologies than the PRODRG server?
>The PRODRG server is great, but since I would like to convert and create topologies for large polymer systems, I can't really limit myself to the 100 atoms allowed.
There is x2top which alas has limited intelligence, and in the current
release is slightly buggy (read: dumps core). However I have a fixed
version which is slightly better.
Then you can make building blocks manually and use pdb2gmx. You then have
to make .rtp and .hdb files, maybe also termini databases.
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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