[gmx-users] gromacs.org_gmx-users Digest, Vol 171, Issue 114

Justin Lemkul jalemkul at vt.edu
Tue Jul 31 20:53:53 CEST 2018

On 7/31/18 2:51 PM, Mohammad Goodarzi wrote:
> Hi Mark,
> Thanks for your reply.I have no idea, the protein structure I got was from
> PDB and the only one with the domain I am interested in.
> How can I add the missing stuff into it and then do the job?
> How can I check for such an error which helps me for future ?

Look for MISSING lines in the PDB file. The error suggests you have at 
least one missing atom that needs to be modeled in before pdb2gmx can 
generate your topology.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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