[gmx-users] Regarding error

Emanuel Birru Emanuel.Birru at monash.edu
Mon Jun 4 08:32:02 CEST 2012

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.


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.birru at monash.edu<mailto:firstname.lastname at monash.edu>

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Seera Suryanarayana
Sent: Monday, 4 June 2012 3:52 PM
To: gmx-users at 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,

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