I wish to perform MDS to DNA molecule for 100 ns time using Gromacs software. Until energy minimization step, i did not get any error. But when i perform NVT step, the error appeared like "Group Protein 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". I have modified molecule name according to input DNA in NVT.mdp. Although, Same error appear again. can you please any one suggest how to modify or create index file? Kindly instruct me for overcome this problem. Herewith, I have attached the NVT.mdp and error screen shot...
Specifying a group named "DNA" should work. GROMACS makes several default groups available. For a simple system of DNA in water, you should not need any index group. The error message you show clearly states the problem is that "Protein" is being used and generates an error. This is clear because a system of DNA and solvent has not protein in it. See the GROMACS manual, section 8.1.1, for available default groups.
Thank you Justine for you Valuable Suggestion. I will follow your instruction.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Software