[gmx-users] atom numbers in top file

[Justin Lemkul]

On 3/21/13 2:12 PM, Shima Arasteh wrote:
> Dear gmx users,
>
> I have modified the top file of my input.pdb. In this modification I have deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved. The atom numbers of deleted atoms are 2 and 3.
> IN grompp I get a fatal error that the top file has not a consecutive numbers and doesn't start from 1.
> Would it be possible to solve this problem? Am I supposed to renumber the atoms and other things manually? Is there any command to renumber the top file? Or is there any other solutions?
>

You need to renumber the topology, and all interactions are affected.  Scripting 
is your friend here.  There is no Gromacs program or command that will do this, 
since modifying topologies in such a way is not normal behavior.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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