[gmx-users] Problem with decane box

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 13 03:42:33 CET 2009

Ragnarok sdf wrote:
> I am trying to set up a system with a helix in a decane box. I am
> using dec50.gro and decane.itp files to build the box. I've used
> GROMOS96 53a6 forcefield and when I run grompp the following error
> comes out.

Hopefully you have modified the decane.itp that you found in the /share/top 
subdirectory; it is for use with ffgmx, which no one should probably be using 

> ERROR 0 [file "vegfr2.top", line 37]:
>   atom C10 (Res C10-107) has mass 0
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: grompp.c, line: 1205
> Fatal error:
> There were 764 errors in input file(s)
> -------------------------------------------------------

You have a crippled topology.  Either the format is wrong, your #include 
statements are wrong, or your [ molecules ] section is out of order...or maybe 
even more possibilities.  With this many errors, it is hard to diagnose without 
actually seeing the topology.


I would appreciate some help on the matter.
> Thank you in advance
> Fabrício Bracht
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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