[gmx-users] Zn problem
David van der Spoel
spoel at xray.bmc.uu.se
Sun Dec 18 10:40:45 CET 2005
hnam wrote:
> In the name of God
> Hello Gromacs users
> I work on adenosine deaminase (ADA). ADA has Zn in its active site and it
> connect to three his and one asp. When I make
> itp file by pdb2gmx , it makes two itp files ,one of them is for protein and
>
> another is for Zn .
> I combined this two itps to one itp file and defined new atom types and new
> his and asp (that are connected to ZN) and also I inserted new parameters in
>
> ffgmxbon.itp and ffgmxbn.itp and aminoaside.dat and ffgmx.rtp and ffgmx.atp
>
> library but when I run grompp it says: fatal error :"no such molecule type
> protein " and source code file :toppush.c line 1264 .Would you please tell
> me everything that I must do.
Check chapter 5 in the manual You have mixed up the order of entries in
the files. You also should use a newer force field if you want to
publish results (referees tend te become more picky about it ).
> Thank you very much in advance
> Institute of Biochemistry and Biophysics (IBB)
> Tehran University
> P.O.box 1417614411
> Tehran
> Iran
>
>
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--
David.
________________________________________________________________________
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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