[gmx-users] CHARMM36 sucrose?

[Justin Lemkul]

On 8/19/14, 8:29 PM, Smith, Micholas D. wrote:
> 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.
>

Does the topology get written, and if so, are the proper bonded interactions 
assigned?

The warnings are not actually important.  The only valid types in 
residuetypes.dat are Protein, DNA, RNA, Ion, and Water.  Anything else gets 
lumped into "Other," which is only really significant if you've got some custom 
residue in the middle of a biopolymer with a different type.

The other thing that you might need to consider is that both your AGLC and BFRU 
have the same residue index (zero), so any bonded interactions in the .rtp that 
use the +/- mechanism probably won't work.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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