[gmx-users] (no subject)

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 12 08:46:13 CEST 2006

lalitha selvam wrote:
> Dear sir,
>    i'm a new user of gromacs.i've done the installation correctly.while
>    simulating my protein i encounter some of the problems.please give me ur
>    suggetions or any reference to overcome this problem.this is my first
>    experience of running the gromacs.kindly look for my problems and 
> answer me
>    as soon as possible.Thanks in advance........some of the errors are..
>    1..while running  pdb2gmx
>        warning :'FE2' not found in residue topology database,trying to use
>    'FE'.i know that i've to use PRODGR to construct topology for Fe.but 
> i'm not
>    familiar to use it.please tell me the procedure of using it.

You need to describe better what you're trying to do with an iron atom, 
and also which force field, for us to suggest a solution. This is not a 
help service for PRODRG, by the way, although some users will have some 
expertise with it. I can only suggest reading whatever documentation it 

>    2..when i'm trying to run grompp
>        Note: System has non-zero total charge : -6.000002e+00.is it 
> necessary
>    to neutralise the charge, if so genion has to run Na means how much 
> i've to
>    add..ie how to calculate it...

Whether you want a neutral system depends what physical model you want 
to use. A physical Na+ ion will have +1e charge. I'll leave it to you to 
work out how many Na+ you need to neutralise -6e :-) (don't worry about 
the tiny fraction).

>    3..with the avialable output file i tried to run mdrun..
>       showing the error that can not open File toplo.tpr but my tpr file is
>    out3.tpr.i'm giving correctly in command also like mdrun -s out3 -o 
> out4 -c
>    out4 -v..........plz give me ur advice to overcome.

Most likely, you aren't giving the command you think you are :-)


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