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
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
|( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
| | feens...@few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "I Am Testing Your Grey Matter" (Red Hot Chili |
| | Peppers) |
|_____________|_______________________________________________________|
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