[gmx-users] Re: Help me about GROMACS

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 21 15:52:09 CEST 2009


With regards to the question about my tutorial, you have not taken care to 
update your topology through the steps of preparing the system.  Using the -p 
flag with genbox and genion will make these changes for you, as is instructed in 
the tutorial.

With regards to your other question, please keep all Gromacs-related 
correspondence unrelated to my tutorial or personal research on the Gromacs 
users list (gmx-users at gromacs.org).  There are numerous tools available for 
creating PDB files, many of them free (PRODRG server, xLeap from AmberTools, etc).


abhijit kayal wrote:
> Hi,
>       I am Abhijit,student  in M.Sc Chemistry at Indian Institute of 
> Technelogy ,Delhi(IITD).
> I was following your tutorial and the following error occur.
> Fatal error:
> number of coordinates in coordinate file (1AKI_solv_ion.gro, 38409)
>              does not match topology (topol.top, 38393)
>                          Could you suggest a solution for this.Another 
> thing is that Iam going to analyse the normal mode of n-butane. So how 
> can I create a PDB file for n- butane.
> Thank you.


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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