The error itself is self explanatory, there are no 22 atoms in your protein structure, that suppose to be there. If you want to ignore those atoms when you build your topology you can use the "-missing" option when you run pdb2gmx. But if you need all the atoms you better construct a complete protein structure using some other software before you run pdb2gmx.
Cheers, ========================================================= Emmanuel Birru PhD Candidate Faculty of Pharmacy and Pharmaceutical Sciences Monash University (Parkville Campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: Int + 61 3 9903 9187 E-mail: emanuel.bi...@monash.edu<mailto:firstname.lastn...@monash.edu> www.pharm.monash.edu.au<http://www.pharm.monash.edu.au/> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Seera Suryanarayana Sent: Monday, 4 June 2012 3:52 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error Dear all gromacs users, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. Suryanarayana Seera, PhD student, Hyderabad, India.
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
