On Tue, 6 May 2008 13:17:29 +0530 (IST)
[EMAIL PROTECTED] wrote:
Dear Users
When I try adding charges (negative charges by adding Cl), using the command
/opt/gromacs/bin/grompp_mpi -np 32 -f em_cc.mdp -po det_em2.mdp -c
1A92_m1_neu.gro -p 1A92_m1.top -o 1A92_m1_em.tpr
it gives me the following error...
-------------------------------------------------------
Program grompp_mpi, VERSION 3.3.1
Source code file: toppush.c, line: 1293
Fatal error:
No such moleculetype CL
-------------------------------------------------------
Could anyone tell me what would be the possible reason for this error?
Simply that the program does not know things you do not tell it!
you need to "#include ions.itp" in you topol.top file.
It looks like you are a beginner with gromacs ... I would advise you
to take the time to go through the tutorial and the wiki to get an
idea of what can be a solution for the problem(sssssss) you will
go through and try to solve them by yourself at least partially.
Using the list to get a quick answer to the step by step process of
setting up a simulation is not the best way to learn.
Thanks in advance
Namitha Mohandas
National Center for Biological Sciences
Tata Institute of Fundamental Research
Bangalore
India
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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