[gmx-users] CHARMM36 sucrose?

Smith, Micholas D. smithmd at ornl.gov
Wed Aug 20 02:33:06 CEST 2014

Hi gmx_users,

I am trying to run a simulation that includes a sucrose molecule constructed with the CHARMM36 AGLC and BFRU carbohydrate residues. The problem is when I run pbd2gmx with the system, the sucrose molecule splits into a separate glucose and fructose molecules, as if it is splitting a chain. It looks like the is that the residues aren't being recognized as chain molecules with the following warnings:

Warning: Warning: Starting residue AGLC0 in chain not identified as Protein/RNA/DNA.

Warning: Starting residue BFRU0 in chain not identified as Protein/RNA/DNA.

Any known solution to this? I've seen that it might be possible to copy-paste the two units together and make a new residue, but this seems like it might be the wrong direction.


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