[gmx-users] Justin-lipid tutorial..

Justin A. Lemkul jalemkul at vt.edu
Sat May 5 15:27:20 CEST 2012

On 5/5/12 4:01 AM, rama david wrote:
> Hi Gromacs Friends,
>   I am doing the justin-lipid tutorial..Link to the tutorial is ...
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
> I made the g96_53a6_lipid force field as per the instruction of tutorial..
> I have some queris regarding to these new force field
> 1.  As we added the lipid parameter to the force field and so
>      I thought to use these force field to dppc to make topology
>      instead of downloading the topol_dppc.top given by justin.
>     So my command line was
>    pdb2gmx -f dppc128.gro -p kkk.top -o kkk.gro -i kkk.itp -ignh
> I got the reply
> Fatal error:
> Something is wrong in the coordinate formatting of file dppc128.gro. Note that
> gro is fixed format (see the manual)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I check the gro format .It is  right as per my knowledge  ..
> What is the reason for such error???

Your impression of the correctness of your .gro file is mistaken.  Something is 
wrong, otherwise pdb2gmx would not complain.  There is also no need to run 
pdb2gmx on a pure DPPC membrane; a simple topology is provided in the tutorial 
for pure lipids.

> And can I used that force field to generate the dppc topology instaed of
> downloading it from tutorial link..
> (As we made the changes in force field to adjust with lipid ....)

If you changed any of the .rtp settings, then you need to use pdb2gmx.  If you 
made changes to dppc.itp, then pdb2gmx will do nothing to help you and you 
should use the approach mentioned above to obtain your topology.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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