you have invoked. It might be "NA" or "Na+" - look at ions.itp and see what the
correct name for the sodium ion is for the force field you are choosing and
make sure it exactly matches the name you used in the topology file. If you are using
a forcefield not explicitly included in ions.itp then you should check the force field
non-bonded parameter file to get the exact name of the sodium atom.
Cheers,
Alan
Date: Wed, 22 Aug 2007 15:02:30 +0530
From: "vijay kumar hinge vijay" <[EMAIL PROTECTED]>
Subject: [gmx-users] error regarding NA+ atom
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Respected sir/madem,
i am using gromacs - 3.1.4 version on sunsolaris platform.i got error at
position restrain at grompp step ,telling dat NO SUCH MOLECULE TYPE
NA+(both are in caps).beofre dat the error which i got , ihv done following
steps
1.first i hv excuted pdb2gmx command den i noted down the charge which given
as out put.charge is -1
2.after editconf(-d 0.9),genbox ,energy minimization(grompp,mdrun) i had
manipulated da .top file by adding #include 'ions.itp,removed one water
molecloe from SOL and added NA+ 1 at da end of topology file .
den i got error after runing da grompp of position restrain ,and i had
changed pr.mdp file ,in that i was added da SOL,0.1,300 (temp)
thanking u for ur patiency
regards
vijaya kumar hinge
Center for Computational Biology
Washington University School of Medicine
700 S. Euclid
St. Louis, MO 63105
(314)-362-2080
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