Question: Cyclodextrin simulation in gromacs
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gravatar for kesav43
2.8 years ago by
kesav430
kesav430 wrote:

Dear friends, I am trying to perform the REMD simulation for the cyclodextrin in gromacs. Buti got error in my first step of converting pdb2gmx. the error is

Warning: Starting residue 0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully


Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/resall.c, line: 642

Fatal error: Residue '' not found in residue topology database


Could you please help me out in solving the error to perform the simulation.

with regards Kesavan Ekambaram

cyclodextrin gromacs • 1.1k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 2.8 years ago by kesav430
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