[gmx-users] CHARMM36 sucrose?
jalemkul at vt.edu
Wed Aug 20 02:40:30 CEST 2014
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
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 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
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