[gmx-users] RE:problem regarding .top file generated by genbox

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 19 08:20:55 CET 2008

sudheer babu wrote:
> Thanks for your reply Mr.justin
> i am sending the commands and .itp file sequence
> the command i have used for protein insertion into membrane  is
> genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro , 
> this command was fine it ran without error.
> Later
> grompp -f em.mdp -c popc_protein.gro(generated by genbox) -p topol.top 
> (generated by genbox) -o em.tpr
> when i ran this grompp command its showing that atom typr NR, HC, CR1 
> not found
>  i am pasting part of my topology file

This is very hard to read. English uses capitalization of names and 
first words in sentences, and punctuation, all to increase readability. 
People are trained to read text where this occurs, and if you do not do 
it then people find your work hard to read. They might well give up on 
reading it, and when you're looking for free help, that's the last thing 
you want to do!

When moving in and out of English (into say, quoting GROMACS commands) 
then you should indicate this with quotation marks "grompp -f em.mdp..." 
, or starting new paragraphs:

   grompp -f em.mdp ...

Yes, this is more work for you, however not doing that work is a false 
economy - you lose people who don't bother to read your post at all.

>        This is your topology file
> ;    "Move Over Hogey Bear" (Urban Dance Squad)
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"

This force field is deprecated. That means you shouldn't be using it 
without a sound reason. It also doesn't define the atom types that 
grompp is complaining about. I guess that you did pdb2gmx on your 
protein with one of the ffGxxx forcefields and are now mixing force 
fields. DON'T! See http://wiki.gromacs.org/index.php/Force_Fields and 
links thereon.

> [ molecules ]
> ; Compound        #mols
> Protein                 1
> POPC                98
> CL-                      3
> SOL               2457

Don't do this either... see http://wiki.gromacs.org/index.php/Thermostats


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