[gmx-users] A promblem when use the x2top
David van der Spoel
spoel at xray.bmc.uu.se
Sun Aug 8 19:57:20 CEST 2004
On Sun, 8 Aug 2004, Hanming wrote:
>I have a very big polymer molecule and try to use x2top to generate a .top
>file. After I relax the molecule and minimized it by other MD and MM
>software , get a .pdb file to do as the input for the x2top. But an error
>always come out like this
>"Fatal error: No forcefield type for atom C6 (1346) with 2 bonds"
>I tried small molecules they are all Ok. But when meet the big one ,error
>always come out. Can I get some suggestion from you about this problem?
copy the file ffgmx.n2t to your directory and edit it to your needs. See
if there is a carbon type with two bonds to appropriate atom types,
otherwise add it.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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