[gmx-users] Re: Need help regarding renumtop
feenstra at few.vu.nl
Mon Jan 16 11:55:23 CET 2012
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
> Kindly help me to overcome this problem. I have also posted it in
> gmxusers (http://firstname.lastname@example.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.
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