Dear Users, I would like to know if anyone may help me understand how to update the index file. I am trying to simulate a dna in solution. I have relaxed a Solvent with attached min.mdp file without problem. in the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But the index file did not work. I have trying to generate an index file using the file.gro from min.mdp but it doesn't work.
Below is the obtained error. Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA_chain_B' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning H bonds into constraints... Velocities were taken from a Maxwell distribution at 10 K ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1332 Fatal error: Group NA+SOL referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I am looking forward to have any suggestion that might help me in this case. I wish all of you a wonderful day. Collins
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