[gmx-users] Re: Need help regarding renumtop

[Anton Feenstra]

On 14/01/12 08:30, Suman Nandy wrote:
> Respected Sir,
>
> According to suggestions, in gmxusers, I have used renumtop, although it
> renumbers the ligand topology, but gives a duplicate atom label.
> ; ERROR: duplicate atom label '4968' for atom #4968 (already used for
> atom #4968)
>
> I used the command "./renumtop topol_Protein_chain_A.itp
> topol_Chain_B.itp".
> Kindly help me to overcome this problem. I have also posted it in
> gmxusers (http://www.mail-archive.com/gmx-users@gromacs.org/msg47032.html)

renumtop is intended to be used with a single molecule topology; so the 
way you use it will not work, as each of the .itp files will contain the 
topology for a molecule (protein chain). Also, renumtop will require 
*unique labels* for all atoms, even though they need not be 
consecutively numbered, and may even be non-numerical.

If you want to create a combined molecule topology for both chains, you 
will first need to (manually) concatenate the corresponding sections 
(atoms, bonds, angles, etc.) of both topology files, and make sure all 
atom number/labels are unique. You might do that by appending 'b' to all 
atom numbers (in all sections) of topol_Chain_B.itp.

P.s., I'm not regularly reading the gmx-users list anymore. If you want 
a response from me, please (also) reply to me directly.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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