[gmx-users] [Fwd: Na.itp problem]

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Sat Dec 24 10:40:49 CET 2005

It is just a game of text. You may rename your molecule type in Na.itp to another name and change the [ molecules ] section accordingly.

Yang Ye

-------- Original Message --------
Subject:     Na.itp problem
Date:     Sat, 24 Dec 2005 12:01:11 +0330
From:     hnam <mahnam at ibb.ut.ac.ir>
To:     David van der Spoel <spoel at xray.bmc.uu.se>

Thank you very much for  your guide.
I replace 9 Na with water in tpr file by genion then fix the topology
file by subtracting 9 from the number of solvent molecules and add 9 Na
when I do grompp with *pr.mdp* ,it says:
Source code file: toppush.c, line: 887
Fatal error:
*moleculetype NA+ is redefined*

This error seems  strange since the molecule type Na is define in
ions.itp.In addition i made a separate  Na.itp and inculde it to top file .
Let me know  what I'm doing wrong.
Thank you very much in advance
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University
P.O.box 1417614411

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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